From sbassi at asalup.org Wed Sep 1 08:36:40 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Wed Sep 1 10:38:25 2004 Subject: [BioPython] Installing Biopython, where is the Makefile? Message-ID: <4135C258.5080905@asalup.org> Hello, I am still working on trying to install Biopython on AMD64. According to several post (and one on this list) I have to compile it with -fPIC option. But I can't find the Makefile.in where I should put this option. Would the Makefile under Bio/KDTree a good place to put it? But I can't find cflags there. I think that switching this parameter is the only thing that is holding me back from compiling Biopython under AMD64. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From mdehoon at ims.u-tokyo.ac.jp Wed Sep 1 21:47:52 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Wed Sep 1 21:48:14 2004 Subject: [BioPython] Installing Biopython, where is the Makefile? In-Reply-To: <4135C258.5080905@asalup.org> References: <4135C258.5080905@asalup.org> Message-ID: <41367BC8.7090305@ims.u-tokyo.ac.jp> Does this error appear with KDTree only, or do you get the same error with other extension modules also? --Michiel. > /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation > R_X86_64_32 can not be used when making a shared object; recompile with > -fPIC > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols: > Bad value > collect2: ld returned 1 exit status > error: command 'g++' failed with exit status 1 Sebastian Bassi wrote: > Hello, > > I am still working on trying to install Biopython on AMD64. > According to several post (and one on this list) I have to compile it > with -fPIC option. > But I can't find the Makefile.in where I should put this option. > Would the Makefile under Bio/KDTree a good place to put it? But I can't > find cflags there. I think that switching this parameter is the only > thing that is holding me back from compiling Biopython under AMD64. > -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From d.lapointe at comcast.net Wed Sep 1 22:09:09 2004 From: d.lapointe at comcast.net (David Lapointe) Date: Wed Sep 1 22:09:41 2004 Subject: [BioPython] Installing Biopython, where is the Makefile? In-Reply-To: <41367BC8.7090305@ims.u-tokyo.ac.jp> References: <4135C258.5080905@asalup.org> <41367BC8.7090305@ims.u-tokyo.ac.jp> Message-ID: <200409012209.09046.d.lapointe@comcast.net> I get this error at KDTree also with Suse 9.1 ( x86_64). That's where the install exits so I don't know about subsequent modules. On Wednesday 01 September 2004 09:47 pm, Michiel Jan Laurens de Hoon wrote: > Does this error appear with KDTree only, or do you get the same error with > other extension modules also? > > --Michiel. > > > /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation > > R_X86_64_32 can not be used when making a shared object; recompile with > > -fPIC > > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols: > > Bad value > > collect2: ld returned 1 exit status > > error: command 'g++' failed with exit status 1 > > Sebastian Bassi wrote: > > Hello, > > > > I am still working on trying to install Biopython on AMD64. > > According to several post (and one on this list) I have to compile it > > with -fPIC option. > > But I can't find the Makefile.in where I should put this option. > > Would the Makefile under Bio/KDTree a good place to put it? But I can't > > find cflags there. I think that switching this parameter is the only > > thing that is holding me back from compiling Biopython under AMD64. -- .david David Lapointe "If you follow the old code of justice - an eye for an eye, a tooth for a tooth- you end up with a blind toothless world" - M Ghandi From mdehoon at ims.u-tokyo.ac.jp Wed Sep 1 22:28:45 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Wed Sep 1 22:27:05 2004 Subject: [BioPython] Installing Biopython, where is the Makefile? In-Reply-To: <200409012209.09046.d.lapointe@comcast.net> References: <4135C258.5080905@asalup.org> <41367BC8.7090305@ims.u-tokyo.ac.jp> <200409012209.09046.d.lapointe@comcast.net> Message-ID: <4136855D.1000203@ims.u-tokyo.ac.jp> I just tried to compile Biopython on my computer. KDTree is actually one of the last extension modules to be compiled; several others (for example Bio.Cluster) are compiled before setup.py reaches KDTree. Did any errors or warnings appear for the extension modules that are compiled before KDTree? David Lapointe wrote: > I get this error at KDTree also with Suse 9.1 ( x86_64). That's where the > install exits so I don't know about subsequent modules. > > > On Wednesday 01 September 2004 09:47 pm, Michiel Jan Laurens de Hoon wrote: > >>Does this error appear with KDTree only, or do you get the same error with >>other extension modules also? >> >>--Michiel. >> >> >>>/usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation >>>R_X86_64_32 can not be used when making a shared object; recompile with >>>-fPIC >>>build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols: >>>Bad value >>>collect2: ld returned 1 exit status >>>error: command 'g++' failed with exit status 1 >> >>Sebastian Bassi wrote: >> >>>Hello, >>> >>>I am still working on trying to install Biopython on AMD64. >>>According to several post (and one on this list) I have to compile it >>>with -fPIC option. >>>But I can't find the Makefile.in where I should put this option. >>>Would the Makefile under Bio/KDTree a good place to put it? But I can't >>>find cflags there. I think that switching this parameter is the only >>>thing that is holding me back from compiling Biopython under AMD64. > > -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From sbassi at asalup.org Thu Sep 2 00:49:03 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Sep 2 00:48:27 2004 Subject: [BioPython] Installing Biopython, where is the Makefile? In-Reply-To: <4136855D.1000203@ims.u-tokyo.ac.jp> References: <4135C258.5080905@asalup.org> <41367BC8.7090305@ims.u-tokyo.ac.jp><200409012209.09046.d.lapointe@comcast.net> <4136855D.1000203@ims.u-tokyo.ac.jp> Message-ID: <59378.12.104.198.106.1094100543.webmail@panel.powered-hosting.com> > I just tried to compile Biopython on my computer. KDTree is actually one > of the > last extension modules to be compiled; several others (for example > Bio.Cluster) > are compiled before setup.py reaches KDTree. Did any errors or warnings > appear > for the extension modules that are compiled before KDTree? I am at the hotel now, tomorrow I will check it back in my workplace. I THINK (NOT SURE!!) there were more complains like this and I got only the last one for the sake of not sending to much program output to the list. Just to get the job done, I cp the /bio and /biodb tree from a working installation (32bits) to this AMD64 computer, and IT WORKED!!! (thanks AMD for making it backward compatible with i686!). It is not the best solution, but at least could make the server work (I had several programs wroten who depends on Biopython). Anyway I will check this tomorrow morning. From sbassi at asalup.org Thu Sep 2 00:53:09 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Sep 2 00:52:27 2004 Subject: [BioPython] Another problem with Biopython compilation on AMD64 In-Reply-To: <200409012206.33980.d.lapointe@comcast.net> References: <083120041454.1403.4134912E000D2D670000057B22007589420A9B0207019F0E04D20B@comcast.net> <200409011907.34383.d.lapointe@comcast.net> <41363F47.6060601@asalup.org> <200409012206.33980.d.lapointe@comcast.net> Message-ID: <59387.12.104.198.106.1094100789.webmail@panel.powered-hosting.com> > Ok my interest is piqued. I'm not at work so I'll have to try this later > but > in the python documentation there is this gem. > http://python.org/doc/current/inst/tweak-flags.html > I can't find any files which would fit into this scheme. I will see this tomorrow. 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Newletter - send a newsletter to all your paying members, unverified members, or simply everyone who has joined. Credit card processing - provides support with paypal payment gateways From mls5w at virginia.edu Wed Sep 8 13:12:28 2004 From: mls5w at virginia.edu (Michael Sierk) Date: Wed Sep 8 13:09:40 2004 Subject: [BioPython] SwissProt parse error Message-ID: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> Hello, all, I'm getting the same error reported last year by Asa Ben Hur ( http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ). I just installed biopython a few weeks ago, and am a newbie with python/biopython. Any suggestions? Thanks, Mike Sierk > wrpmg4b:~ % python disulfides2.py test_seqs.aln > Swissprot ID: Q14063 > Traceback (most recent call last): > File "disulfides2.py", line 73, in ? > seq_record = get_sprot_entry_remote(seq_id) > File "disulfides2.py", line 26, in get_sprot_entry_remote > entry = iterator.next() > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next > return self._parser.parse(File.StringHandle(data)) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse > self._scanner.feed(handle, self._consumer) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed > self._scan_record(uhandle, consumer) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in > _scan_record > fn(self, uhandle, consumer) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in > _scan_reference > self._scan_ra(uhandle, consumer) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in _scan_ra > one_or_more=1) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in > _scan_line > read_and_call(uhandle, event_fn, start=line_type) > File > "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ > python2.3/site-packages/Bio/ParserSupport.py", line 300, in > read_and_call > raise SyntaxError, errmsg > SyntaxError: Line does not start with 'RA': > RX DOI=10.1146/annurev.nutr.22.012502.114457; ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ Michael Sierk, Postdoctoral Fellow email: mls5wvirginiaedu Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 University of Virginia (H): (434) 970-2268 ------------------------------------------------------------------------ ------ "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ From idoerg at burnham.org Wed Sep 8 13:50:32 2004 From: idoerg at burnham.org (Iddo) Date: Wed Sep 8 13:50:45 2004 Subject: [BioPython] SwissProt parse error In-Reply-To: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> References: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> Message-ID: <413F4668.3010100@burnham.org> Hey Mike, Asa was using an old version of biopython, and that sorted itself out. However, he was parsing a local file. Are you parsing a local or one you are reading from the ExPasy website? Anyhow, if you email me a bare-bones version of your source code, I'll have a looksee. Iddo The problem then was that Asa was using an old version... but if you Michael Sierk wrote: > Hello, all, > > I'm getting the same error reported last year by Asa Ben Hur ( > http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ). > I just installed biopython a few weeks ago, and am a newbie with > python/biopython. Any suggestions? > > Thanks, > Mike Sierk > >> wrpmg4b:~ % python disulfides2.py test_seqs.aln >> Swissprot ID: Q14063 >> Traceback (most recent call last): >> File "disulfides2.py", line 73, in ? >> seq_record = get_sprot_entry_remote(seq_id) >> File "disulfides2.py", line 26, in get_sprot_entry_remote >> entry = iterator.next() >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next >> return self._parser.parse(File.StringHandle(data)) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse >> self._scanner.feed(handle, self._consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed >> self._scan_record(uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in >> _scan_record >> fn(self, uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in >> _scan_reference >> self._scan_ra(uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in _scan_ra >> one_or_more=1) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in >> _scan_line >> read_and_call(uhandle, event_fn, start=line_type) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/ParserSupport.py", line 300, in >> read_and_call >> raise SyntaxError, errmsg >> SyntaxError: Line does not start with 'RA': >> RX DOI=10.1146/annurev.nutr.22.012502.114457; > > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > Michael Sierk, Postdoctoral Fellow email: > mls5wvirginiaedu > Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 > University of Virginia (H): (434) 970-2268 > ------------------------------------------------------------------------ > ------ > "There is something fascinating about science. One gets such wholesome > returns of conjecture out of such a trifling investment of fact." > -- Mark Twain. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From idoerg at burnham.org Wed Sep 8 13:53:27 2004 From: idoerg at burnham.org (Iddo) Date: Wed Sep 8 13:53:38 2004 Subject: [BioPython] SwissProt parse error In-Reply-To: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> References: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> Message-ID: <413F4717.4000807@burnham.org> Silly me, you are parsing a local file, I just looked better at the stack dump. Michael Sierk wrote: > Hello, all, > > I'm getting the same error reported last year by Asa Ben Hur ( > http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ). > I just installed biopython a few weeks ago, and am a newbie with > python/biopython. Any suggestions? > > Thanks, > Mike Sierk > >> wrpmg4b:~ % python disulfides2.py test_seqs.aln >> Swissprot ID: Q14063 >> Traceback (most recent call last): >> File "disulfides2.py", line 73, in ? >> seq_record = get_sprot_entry_remote(seq_id) >> File "disulfides2.py", line 26, in get_sprot_entry_remote >> entry = iterator.next() >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next >> return self._parser.parse(File.StringHandle(data)) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse >> self._scanner.feed(handle, self._consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed >> self._scan_record(uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in >> _scan_record >> fn(self, uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in >> _scan_reference >> self._scan_ra(uhandle, consumer) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in _scan_ra >> one_or_more=1) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in >> _scan_line >> read_and_call(uhandle, event_fn, start=line_type) >> File >> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >> python2.3/site-packages/Bio/ParserSupport.py", line 300, in >> read_and_call >> raise SyntaxError, errmsg >> SyntaxError: Line does not start with 'RA': >> RX DOI=10.1146/annurev.nutr.22.012502.114457; > > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > Michael Sierk, Postdoctoral Fellow email: > mls5wvirginiaedu > Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 > University of Virginia (H): (434) 970-2268 > ------------------------------------------------------------------------ > ------ > "There is something fascinating about science. One gets such wholesome > returns of conjecture out of such a trifling investment of fact." > -- Mark Twain. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From jonathan.taylor at utoronto.ca Tue Sep 7 01:08:13 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Wed Sep 8 17:32:41 2004 Subject: [BioPython] Patch to give access to return codes of apps run through biopython Message-ID: <1094533693.5218.3.camel@localhost.localdomain> Hi, I needed the return code off of primer3 so heres the patch for cvs I am using. I don't think this breaks anything and adds some useful functionality. Cheers. Jon. -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython_patch-access_to_return_code_of_applications.diff Type: text/x-patch Size: 2048 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040907/ed3d0d4e/biopython_patch-access_to_return_code_of_applications.bin From jonathan.taylor at utoronto.ca Tue Sep 7 14:56:47 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Wed Sep 8 17:32:42 2004 Subject: [BioPython] Patch for ApplicationResult Message-ID: <1094583372.3817.3.camel@dallas.bbc.botany.utoronto.ca> This adds the useful return value to ApplicationResult. My earlier message did not make it to the list so I am trying to rephrase it. Jon. -------------- next part -------------- A non-text attachment was scrubbed... Name: biopython_patch-access_to_return_code_of_applications.diff Type: text/x-patch Size: 2048 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040907/b9ba6e5c/biopython_patch-access_to_return_code_of_applications.bin From jeffrey_chang at stanfordalumni.org Wed Sep 8 17:49:48 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Wed Sep 8 17:50:01 2004 Subject: [BioPython] SwissProt parse error In-Reply-To: <413F4668.3010100@burnham.org> References: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> <413F4668.3010100@burnham.org> Message-ID: <01684F51-01E1-11D9-8990-000A956845CE@stanfordalumni.org> Hi Mike, Yes, what Iddo said. Please grab the latest SProt.py code from the latest CVS (cvs.biopython.org) and see if that solves your problem. Also, I have committed a fix today to handle recent format changes in swiss-prot, that was reported in personal correspondence by Daan Archer. They have added an "RG" field. I don't know whether that is causing the problem. If not, please let us know what swiss-prot record is failing to parse. Thanks, Jeff On Sep 8, 2004, at 1:50 PM, Iddo wrote: > > Hey Mike, > > Asa was using an old version of biopython, and that sorted itself out. > However, he was parsing a local file. Are you parsing a local or one > you are reading from the ExPasy website? > > Anyhow, if you email me a bare-bones version of your source code, I'll > have a looksee. > > Iddo > > > The problem then was that Asa was using an old version... but if you > > Michael Sierk wrote: > >> Hello, all, >> >> I'm getting the same error reported last year by Asa Ben Hur ( >> http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html >> ). >> I just installed biopython a few weeks ago, and am a newbie with >> python/biopython. Any suggestions? >> >> Thanks, >> Mike Sierk >> >>> wrpmg4b:~ % python disulfides2.py test_seqs.aln >>> Swissprot ID: Q14063 >>> Traceback (most recent call last): >>> File "disulfides2.py", line 73, in ? >>> seq_record = get_sprot_entry_remote(seq_id) >>> File "disulfides2.py", line 26, in get_sprot_entry_remote >>> entry = iterator.next() >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next >>> return self._parser.parse(File.StringHandle(data)) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse >>> self._scanner.feed(handle, self._consumer) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed >>> self._scan_record(uhandle, consumer) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in >>> _scan_record >>> fn(self, uhandle, consumer) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in >>> _scan_reference >>> self._scan_ra(uhandle, consumer) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in >>> _scan_ra >>> one_or_more=1) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in >>> _scan_line >>> read_and_call(uhandle, event_fn, start=line_type) >>> File >>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>> python2.3/site-packages/Bio/ParserSupport.py", line 300, in >>> read_and_call >>> raise SyntaxError, errmsg >>> SyntaxError: Line does not start with 'RA': >>> RX DOI=10.1146/annurev.nutr.22.012502.114457; >> >> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> ++ +++++++ >> Michael Sierk, Postdoctoral Fellow email: >> mls5wvirginiaedu >> Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 >> University of Virginia (H): (434) 970-2268 >> ---------------------------------------------------------------------- >> -- ------ >> "There is something fascinating about science. One gets such wholesome >> returns of conjecture out of such a trifling investment of fact." >> -- Mark Twain. >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> ++ +++++++ >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython >> >> > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From mls5w at virginia.edu Thu Sep 9 11:55:17 2004 From: mls5w at virginia.edu (Michael Sierk) Date: Thu Sep 9 11:51:58 2004 Subject: [BioPython] SwissProt parse error In-Reply-To: <01684F51-01E1-11D9-8990-000A956845CE@stanfordalumni.org> References: <4326EDD2-01BA-11D9-82EE-003065C04818@virginia.edu> <413F4668.3010100@burnham.org> <01684F51-01E1-11D9-8990-000A956845CE@stanfordalumni.org> Message-ID: The parsing problem is solved. Thanks! Mike On Sep 8, 2004, at 5:49 PM, Jeffrey Chang wrote: > Hi Mike, > > Yes, what Iddo said. Please grab the latest SProt.py code from the > latest CVS (cvs.biopython.org) and see if that solves your problem. > Also, I have committed a fix today to handle recent format changes in > swiss-prot, that was reported in personal correspondence by Daan > Archer. They have added an "RG" field. I don't know whether that is > causing the problem. If not, please let us know what swiss-prot > record is failing to parse. > > Thanks, > Jeff > > > On Sep 8, 2004, at 1:50 PM, Iddo wrote: > >> >> Hey Mike, >> >> Asa was using an old version of biopython, and that sorted itself >> out. However, he was parsing a local file. Are you parsing a local >> or one you are reading from the ExPasy website? >> >> Anyhow, if you email me a bare-bones version of your source code, >> I'll have a looksee. >> >> Iddo >> >> >> The problem then was that Asa was using an old version... but if you >> >> Michael Sierk wrote: >> >>> Hello, all, >>> >>> I'm getting the same error reported last year by Asa Ben Hur ( >>> http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html >>> ). >>> I just installed biopython a few weeks ago, and am a newbie with >>> python/biopython. Any suggestions? >>> >>> Thanks, >>> Mike Sierk >>> >>>> wrpmg4b:~ % python disulfides2.py test_seqs.aln >>>> Swissprot ID: Q14063 >>>> Traceback (most recent call last): >>>> File "disulfides2.py", line 73, in ? >>>> seq_record = get_sprot_entry_remote(seq_id) >>>> File "disulfides2.py", line 26, in get_sprot_entry_remote >>>> entry = iterator.next() >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next >>>> return self._parser.parse(File.StringHandle(data)) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse >>>> self._scanner.feed(handle, self._consumer) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed >>>> self._scan_record(uhandle, consumer) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in >>>> _scan_record >>>> fn(self, uhandle, consumer) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in >>>> _scan_reference >>>> self._scan_ra(uhandle, consumer) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in >>>> _scan_ra >>>> one_or_more=1) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in >>>> _scan_line >>>> read_and_call(uhandle, event_fn, start=line_type) >>>> File >>>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ >>>> python2.3/site-packages/Bio/ParserSupport.py", line 300, in >>>> read_and_call >>>> raise SyntaxError, errmsg >>>> SyntaxError: Line does not start with 'RA': >>>> RX DOI=10.1146/annurev.nutr.22.012502.114457; >>> >>> >>> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> +++ +++++++ >>> Michael Sierk, Postdoctoral Fellow email: >>> mls5wvirginiaedu >>> Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 >>> University of Virginia (H): (434) 970-2268 >>> --------------------------------------------------------------------- >>> --- ------ >>> "There is something fascinating about science. One gets such >>> wholesome >>> returns of conjecture out of such a trifling investment of fact." >>> -- Mark Twain. >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> +++ +++++++ >>> >>> _______________________________________________ >>> BioPython mailing list - BioPython@biopython.org >>> http://biopython.org/mailman/listinfo/biopython >>> >>> >> >> >> -- >> Iddo Friedberg, Ph.D. >> The Burnham Institute >> 10901 N. Torrey Pines Rd. >> La Jolla, CA 92037 USA >> Tel: +1 (858) 646 3100 x3516 >> Fax: +1 (858) 713 9930 >> http://ffas.ljcrf.edu/~iddo >> >> _______________________________________________ >> BioPython mailing list - BioPython@biopython.org >> http://biopython.org/mailman/listinfo/biopython >> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ Michael Sierk, Postdoctoral Fellow email: mls5wvirginiaedu Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 University of Virginia (H): (434) 970-2268 ------------------------------------------------------------------------ ------ "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ From test at latinmail.com Thu Sep 9 12:11:39 2004 From: test at latinmail.com (test@latinmail.com) Date: Thu Sep 9 12:11:40 2004 Subject: [BioPython] Dating Software $199 Message-ID: <200409091611.i89GBYKs011336@portal.open-bio.org> I am offering a Dating Website Software $199 USD If you are interested please contact me using plpmauto@yahoo.com ONLY serious offers please. More Info below.... Client Area Below are the client area features of the dating Software. Your dating site members will be able to use all the functions described below to find and contact their matches. If you'd like to try these features on a live demo General Features Member’s Login Error Trap Capability Advanced Search Features. 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Billing History - lets members see what payments they have previously made. Search Features Basic Search - search members based on specific criteria including age, location, and profiles that have pictures only. Four types of searches can be performed by members: Quick Search - a basic search made for ease of use. Username Search - search for a specific member based on member number. Advanced Search - a search that lets a member search for others based on very detailed profile criteria to find the perfect match. Whos Online. show users online with basic profile information Administrative Area Web based configuration - the web based configuration allows you to edit configurations, admin password, pricing. Member Management - allows you to manage your existing members and change any aspect of their profile, from description content to modifying the expiration of their subscription. Newletter - send a newsletter to all your paying members, unverified members, or simply everyone who has joined. Credit card processing - provides support with paypal payment gateways From crocha at dc.uba.ar Thu Sep 9 14:39:32 2004 From: crocha at dc.uba.ar (Cristian Sebastian Rocha) Date: Thu Sep 9 14:44:54 2004 Subject: [BioPython] BioCM Message-ID: <3574.157.86.8.239.1094755172.squirrel@webmail.dc.uba.ar> Hi everybody, I just start the registry of a new project in Sourceforge.org. The following is a simple description of it. If you think it?s usefull for you, please join to the proyect: I need help! I will upload the code to the CVS of sourceforge when the proyect be available. thanks! Cristian. Project Information ------------------- 1. Submitter: csrocha 2. Project UNIX Name: biocm 3. Project Descriptive Name: Biological Content Management 4. License: GNU General Public License (GPL) License other: 5. Project Description: BioCM is Biological Content Manager: a Zope/Plone/Biopython product to manage, share and publish biological annotations on the web. 6. Registration Description: Bioinformatics and Molecular Biology Laboratories requires access to databases and scripts to manipulate big repositories of biological information. Usually each bioinformatics and biologists researchers populate local databases/filesystems with a reduced set of biological information without share and content search capacities. These result is a non optimized use of recurses with thousand of copy of information (one of each researcher) in the local filesystems for each bioinformatics laboratories, and a heavy process to synchronize data between researchers. Exists tools, as NTI-Vector (not GNU), with workgroup capacities can?t publish the results on the web: an important feature for laboratories who want to share they results with others. The main aim of this proyect is to build a workgroup tool to manage biological informaction with web publishing capacities. That is possible using Zope/Plone workgroup and web publishing features. Biopython is the tool to manage of biological information in a easy way. -- Lic. Cristian S. Rocha Universidad de Buenos Aires, FCEyN, Departamento de Computaci?n. From jonathan.taylor at utoronto.ca Fri Sep 10 13:06:49 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Fri Sep 10 13:08:04 2004 Subject: [BioPython] Contributing code to cvs Message-ID: <1094836009.8912.2.camel@dallas.bbc.botany.utoronto.ca> I have 2 questions: 1 - My messages keep getting delayed on the way to the list because the headers look like spam. Is there any way this can be disabled? 2 - I am currently doing a lot of work with biopython and have implemented a few patches against biopython CVS head to make my life easier. I am willing to submit patches. I sent one earlier, but no one has responded yet. Is biopython open for external contributation? Thanks for the great toolkit. Cheers. Jon. From kingsley at eurotelecom.ru Fri Sep 10 14:32:42 2004 From: kingsley at eurotelecom.ru (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Sep 10 14:56:04 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dog0dPCxc3I0NsgyiDC29HS?= =?windows-1251?b?wMLKxQ==?= Message-ID: <113485678.20040910183742@> ???????? ? ???????? ????? ???????????? ?????? ? ?????????? ? 1 ???? 1000 ??. - 411 ?.?. ?????????-?????, ????????? 1 ???? 1000 ??. - 364 ?.?. ?????? ??????????? ? ???????????? ???????? 1000 ?? - 418 ?.?. ??????-???????, ????????? 1 ???? 1000 ??. - 634 ?.?. ???????? ? ?????????? ? 2 ????? 100 ??. - 417 ?.?. ????? ? ?????????? ? 1 ???? 500 ??. - 598 ?.?. ?????? ? ???????????? ?????????????? ???????? 1000 ??. - 457 ?.?. ?????????, 3 ??????, 1000 ??. - 326 ?.?. ?????? 40?50 ??? 30?40 ?? ? ?????????? ? 1 ????, 1000 ??. - 229 ?.?. ?????????? ?????? ??? ????????? ?? 30 ?.?. ? ????? ?????????, ??????, ?????, ????????, ??????? ??? ????. ?????, ????????? ????, ?????????, ???????????, ??????, ??????????-????? ? ?????? ??????. ?????????? ? ???????? ???????? ?4, ????????? 4+4, 1000 ?? - 246 ?.?. 3000 ?? - 318 ?.?. ??????? ?4, 2 ??????, ????????? 4+4, 1000 ??. - 252 ?.?. 3000 ??. - 328 ?.?. ??????? 2+0 500 ??. - 113 ?.?. ????????? ??????, 2 ?????, 2000 ??. - 99 ?.?. ??????????? ????????? ??????????? 3000 ??. - 213 ?.?. ????? ?? ??????? ? ????????? 500 ??. - 426 ?.?. ????? ????????? (??????) ? ????????? 500 ??. - 281 ?.?. ?????????- ????? 500 ??. - 277 ?.?. ????????? ????????? 500 ??. - 338 ?.?. ?????????? ?????? ??? ???????? ????????? ?? 70 ?.?. ????????? ??????????? ?????? ?? 1000 ?.?. ?????? ?????? ?? 500 ?.?. ??????????? ????? ??????, ?? ????????: (095) 7-888-769 (095) 101-3527 (????????.) ? ??? ????????? ??????? ??? ??????????? ? ?????????? ? ?????????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From postmaster at communitymemorial.com Mon Sep 13 06:36:34 2004 From: postmaster at communitymemorial.com (System Administrator) Date: Mon Sep 13 06:33:58 2004 Subject: [BioPython] Undeliverable: Re: Failure Message-ID: Your message To: domzil@communitymemorial.com Subject: Re: Failure Sent: Mon, 13 Sep 2004 05:33:29 -0500 did not reach the following recipient(s): domzil@communitymemorial.com on Mon, 13 Sep 2004 05:36:31 -0500 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=cmh;l=CMHMAIL020409131036SQJ254DR MSEXCH:IMS:CMH:CMHMF:CMHMAIL02 0 (000C05A6) Unknown Recipient From ambrose at t-online.de Mon Sep 13 15:51:32 2004 From: ambrose at t-online.de (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Mon Sep 13 16:09:48 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogyu7s7/z+8uXw7fvpIPHl?= =?windows-1251?b?8OLo8SDoIOzg8Orl8ujt4yEgIM/w7uTg5uAg7e7z8uHz6u7iIQ==?= Message-ID: <175559721.20040913195632@> ???????????? ?????? ? ?????????! ??????? ?????????! ????????? ???????????? ??????? Windows'98/2000/NT/XP - ?? 30 ?.?. ?????, ????????? ? ????????? ?????? ???????????? ??????????? - ?? 520 ???. ?? ?????????. ??????????? ????????????? ????? - ?? 15 ?.?. ?? 55 ?.?. (?? 1 ????). ????????? ????? - 650 ??? ? ???. ?????????????? ?????? - ?? 30 ?.? ?? 350 ?.?. ????? ? ??????????? ???? ??????? - ?? 960 ???. ? ???. ??????????? ? ???????? ? ????????? "??? ????" - ?? 940 ???. ??????????? ???????????? 1-3 ?????? ? ???. - ?? 75 ?.?. (????? ? ??????? 2-3 ?????!) ???????? ????????? ???? ? ????? ? ???????????? ????????? ??? ??????????? ???????. ?????? ? ????????? - ?? 150 ?.?. (4 ?????). ???????????????? ?? ?????? ???????-?????????? (???????? ???? ??????????? ? ?????????) - ?? 20 ?.?. ?? 60 ?.?. ???????????????? ?? web - ??????? - ?? 55 ?.?. ?? ???? ??????????? ???????? ???? ? ????????? ????? ????????? (.ru, .su, .com, net, .org, .biz, .info, .edu, .tv, .cc, .ws, .bz, .name, .tm, .aero, coop, .museum, .pro, ? ? ???? .??, .???, .???, .???) - ?? 20 ?.?. ? ???. ?? 1.500.000 ?.?. WEB - ?????? (???????? ??????, ???????? ?? ?????, web - ???????????? ?? ?????, ????????? ???????? ? ???????? ?? ????) - ?? 50 ?.?. ?? 25.000 ?.?. ???????????????? ?? ???????? ???????????? ???????????? - ?? 25 ?.?. ?? 780 ?.?. ???????????? ? ???????? ?? ??????, ?????????, ?????????? - ?? 15 ?.?. ?? 195 ?.?. ????????-?????????, ?????? ???????????? ?????, ???????????????? ?? ????? (??????????? ????????????) - ?? 700 ?.?. ?? 5.900 ? ?????. ??????? ? ????????, ?????????, ???????????, ?????????? ?????? ?? ??? ???? ? ????????? ? ??????????? - ?? 300 ?.?. ?? 1.700 ? ????? ?????? ?? ??????????? ?????? ????? - ?? 200 ?.?. ?? 12.000 ?.?. ??????? ???????? ????? ???????????? ?? ???????????? ???????! ????? ??????? ? ??????? 1 ???! ???????? ? ????????? ? ???????? ???! ???.: (095) 976-9092, 7-888-769 ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From moorhty at t-online.de Tue Sep 14 11:32:57 2004 From: moorhty at t-online.de (elmootaz) Date: Tue Sep 14 11:56:24 2004 Subject: [BioPython] =?windows-1251?b?ze7i4P8g6u7r6+Xq9uj/?= Message-ID: <200409141556.i8EFuEKr009532@portal.open-bio.org> ????? ????????? ??????????? ????? ?? ????? www.elitpresent.ru From longlill at yahoo.com Wed Sep 15 07:02:10 2004 From: longlill at yahoo.com (Long Li) Date: Wed Sep 15 07:02:07 2004 Subject: [BioPython] BioPython Homepage: Links not easily seen Message-ID: <20040915110210.55925.qmail@web52802.mail.yahoo.com> Hi, It is not easy to see the links when browsing BioPython homepage. I have to move the mouse to the text to know if it is a link. Could those links be underlined like BioPerl homepage or be displayed in another color? Best regards, Long __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From macrozhu at gmail.com Wed Sep 15 08:02:51 2004 From: macrozhu at gmail.com (Hongbo Zhu) Date: Wed Sep 15 08:02:49 2004 Subject: [BioPython] routine retrieve_pdb_file() from Bio.PDB.PDBList store PDB file in a local file anyway. Message-ID: <11b97ec040915050270229875@mail.gmail.com> Hi, I found the routine retrieve_pdb_file() from Bio.PDB.PDBList store PDB file in a local file anyway, even if you set parameter "write" to 0. I checked the souce code and I found the parameter "write" is not checked in the routine. Could this be a bug? regards -- Macro Zhu macrozhu at gmail.com From longlill at yahoo.com Wed Sep 15 08:27:50 2004 From: longlill at yahoo.com (Long Li) Date: Wed Sep 15 08:27:49 2004 Subject: [BioPython] routine retrieve_pdb_file() from Bio.PDB.PDBList store PDB file in a local file anyway. In-Reply-To: <11b97ec040915050270229875@mail.gmail.com> Message-ID: <20040915122750.16089.qmail@web52810.mail.yahoo.com> Download the latest PDBList.py module file from the cvs. Thomas has fixed it. Good luck, Long --- Hongbo Zhu wrote: > Hi, > > I found the routine retrieve_pdb_file() from > Bio.PDB.PDBList store PDB > file in a local file anyway, even if you set > parameter "write" to 0. I > checked the souce code and I found the parameter > "write" is not > checked in the routine. Could this be a bug? > > regards > -- > Macro Zhu > macrozhu at gmail.com > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From yon at ujsa.com Wed Sep 15 10:04:22 2004 From: yon at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Wed Sep 15 10:09:45 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dog0dPCxc3I0NsgyiDC29HS?= =?windows-1251?b?wMLKxQ==?= Message-ID: <116464434.20040915140922@> ???????? ? ???????? ????? ???????????? ?????? ? ?????????? ? 1 ???? 1000 ??. - 411 ?.?. ?????????-?????, ????????? 1 ???? 1000 ??. - 364 ?.?. ?????? ??????????? ? ???????????? ???????? 1000 ?? - 418 ?.?. ??????-???????, ????????? 1 ???? 1000 ??. - 634 ?.?. ???????? ? ?????????? ? 2 ????? 100 ??. - 417 ?.?. ????? ? ?????????? ? 1 ???? 500 ??. - 598 ?.?. ?????? ? ???????????? ?????????????? ???????? 1000 ??. - 457 ?.?. ?????????, 3 ??????, 1000 ??. - 326 ?.?. ?????? 40?50 ??? 30?40 ?? ? ?????????? ? 1 ????, 1000 ??. - 229 ?.?. ?????????? ?????? ??? ????????? ?? 30 ?.?. ? ????? ?????????, ??????, ?????, ????????, ??????? ??? ????. ?????, ????????? ????, ?????????, ???????????, ??????, ??????????-????? ? ?????? ??????. ?????????? ? ???????? ???????? ?4, ????????? 4+4, 1000 ?? - 246 ?.?. 3000 ?? - 318 ?.?. ??????? ?4, 2 ??????, ????????? 4+4, 1000 ??. - 252 ?.?. 3000 ??. - 328 ?.?. ??????? 2+0 500 ??. - 113 ?.?. ????????? ??????, 2 ?????, 2000 ??. - 99 ?.?. ??????????? ????????? ??????????? 3000 ??. - 213 ?.?. ????? ?? ??????? ? ????????? 500 ??. - 426 ?.?. ????? ????????? (??????) ? ????????? 500 ??. - 281 ?.?. ?????????- ????? 500 ??. - 277 ?.?. ????????? ????????? 500 ??. - 338 ?.?. ?????????? ?????? ??? ???????? ????????? ?? 70 ?.?. ????????? ??????????? ?????? ?? 1000 ?.?. ?????? ?????? ?? 500 ?.?. ??????????? ????? ??????, ?? ????????: (095) 7-888-769 (095) 101-3527 (????????.) ? ??? ????????? ??????? ??? ??????????? ? ?????????? ? ?????????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From longlill at yahoo.com Wed Sep 15 10:15:17 2004 From: longlill at yahoo.com (Long Li) Date: Wed Sep 15 10:15:27 2004 Subject: [BioPython] bug: PDB.PDBList module "get_recent_filenames" Message-ID: <20040915141517.61563.qmail@web52810.mail.yahoo.com> In PDB.PDBList module, the method "get_recent_filenames" of the class "PDBList" has a bug. ____________________________________________________ def get_recent_filenames(self): ... ... file = url.readlines() maxdate = 0 for l in file: try: # check if this is a valid date date = int(l[54:62]) if date > maxdate: maxdate = date except: pass ... ... _____________________________________________________ The statement "date = int(l[54:62])" should be changed to "date = int( l[ 45:53 ] )". After I try the statement "file = url.readlines()" in the code above, it output like this: drwxrwxr-x 2 702 512 Aug 30 19:22 20040830 drwxrwxr-x 2 702 512 Sep 3 16:06 20040903 drwxrwxr-x 2 702 512 Sep 13 17:03 20040913 -rw-r--r-- 1 702 1218 Nov 26 2003 README not like that described in the module: drwxrwxr-x 2 1002 sysadmin 512 Oct 6 18:28 20031006 drwxrwxr-x 2 1002 sysadmin 512 Oct 14 02:14 20031013 -rw-r--r-- 1 1002 sysadmin 1327 Mar 12 2001 README I think it is not a good way to get the directory name by using the slice of result of "readlines()", could the directory name be read directly? Best regards, Long __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From jonathan.taylor at utoronto.ca Wed Sep 15 19:36:20 2004 From: jonathan.taylor at utoronto.ca (Jonathan Taylor) Date: Wed Sep 15 19:36:15 2004 Subject: [BioPython] Patch for ApplicationResult - Someone going to look at this? In-Reply-To: <1094583372.3817.3.camel@dallas.bbc.botany.utoronto.ca> References: <1094583372.3817.3.camel@dallas.bbc.botany.utoronto.ca> Message-ID: <1095291380.28232.2.camel@localhost.localdomain> I also have more patches I would be willing to contribute. jon. On Tue, 2004-09-07 at 14:56, Jonathan Taylor wrote: > This adds the useful return value to ApplicationResult. > > My earlier message did not make it to the list so I am trying to > rephrase it. > > Jon. > > ______________________________________________________________________ > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From gautam at surrealismo.com Wed Sep 15 21:47:53 2004 From: gautam at surrealismo.com (wen-jing) Date: Wed Sep 15 22:06:08 2004 Subject: [BioPython] =?windows-1251?b?z+7q8+/q6A==?= Message-ID: <200409160206.i8G25vKr006183@portal.open-bio.org> ???????? ? ?????? ??????? ???? ? ??????? ?????! http://pokupki.net From mhullgx at cursor.nl Thu Sep 16 03:42:29 2004 From: mhullgx at cursor.nl (Mervin Hull) Date: Thu Sep 16 04:27:30 2004 Subject: [BioPython] Small-Cap With High Potential? Message-ID: Automotive Capital GR0UP, Inc.(OTC: AOCP) Offers Future Guidance Of $0.30 Earnings Per Share With $8 MILLI0N Revenue Over Next 12 Months. Imagine how well your portfolio would have done if you had the scoop on the following stocks: (OTC:AUML):Closed July 9th at $.10. Traded over $4.00 on August 4th. Ama-zing.(Split 5 for 1 August 5th) Do the math.You may not know a lot about investing, but we're sure you can count. (OTC:EMTK):Closed August 10th at $.10. Closed September 2nd at $.84, up 740% in a few weeks! Think some overowned, overblown stock like Intel is going to move like that anytime soon? Ordinary Investors Like You are Turbocharging Their Portfolios With Select High Potential Microcap Stocks. Some of these stocks really do fly. And that's what you as an investor ultimately care about. Let's Look at Today's Featured Company, Automotive Capital GR0UP, Inc.(OTC: AOCP): Automotive Capital GR0UP, Inc. (OTC:AOCP) is a small publicly traded automotive holding company established to invest in all aspects of automotive retailing and finance including franchised new car dealerships, independent used car dealerships, b.uy-here pay-here dealerships, specialty finance companies including sub-prime lenders and car title loan companies, premium finance companies that finance commercial auto in-surance premiums and F&I marketing companies that market all aspects of dealership F&I and the automotive aftermarket. In these early stages we are placing special emphasis on providing solutions in in-surance premium finance, automotive specialty financing including the originating of consumer loans as well as purchasing sub-prime loan portfolios, car title loans and exotic auto loans through our 100% owned corporate subsidiaries, Auto Capital Financial Corp, an Arizona Sales Finance Company (application pending), and Premium Assurance Company, an Arizona Premium Finance Company (application pending). (Source: Company Website) Reason to Consider This Stock: News Announcement September 2nd, 2004: *Automotive Capital GR0UP, Inc. Executes Merger Agreement With Colfax and Navicom and Begins Booking Sales and Revenue. Here is an excerpt from that announcement: SCOTTSDALE, Ariz., Sept. 2 /PRNewswire-FirstCall/ -- Automotive Capital GR0UP, Inc. (OTC: AOCP - News) today announced the execution of the agreement between Automotive Capital GR0UP, Inc., Colfax Financial and Navicom GPS. Automotive Capital GR0UP, Inc. began booking sales and revenue as of September 1, 2004. This merger allows AOCP to have $0.30 earnings per share (EPS) and over $8 MILLI0N in revenue over the next 12 months. The company will have about $5 MILLI0N in assets with 8 million fully diluted shares outstanding. The company owns two automobile dealer lots in Arizona, and Navicom, a growing innovative wireless GPS technology that works in 98% of the US, Canada and Mexico. The company also announced the launch of Navicom's wireless GPS marketing campaign for homeland security agencies, law enforcement, government agencies, auto dealers, fleet managers and trucking companies. Navicom announced last week that it is providing units and monthly service to the Inspector General's Office in Washington, D.C. Navicom foresees the $25 BILLI0N sub-prime automobile market becoming the fastest growing segment and will of-fer companies its asset collateral monitoring devices with lease options. These solutions include automobile tracking, auto disable/enable capability through Internet, geo-fence boundary notification and point/cl-ick auto repossession. Other sub-prime auto companies are also buying Navicom to install on vehicles they finance. Read the other announcements on this Company! Do your homework on this stock! Many of these small unknown companies absolutely EXPLODE onto investor's radar screens and the stock of many absolutely soar! Look at the examples above. Like many of these unknown stocks, one major news announcement and AOCP could go ballistic! Is AOCP poised to blaze higher? If you think so, you may want to take action immediately.... Good Luck and successful investing. DIS-CLAIMER: Information within this email contains "F0RWARD looking statements" within the meaning of Section 27A of the Securities Act of 1933 and Section 21B of the Securities Exchange Act of 1934. Any statements that express or involve discussions with respect to predictions, expectations, beliefs, plans, projections, objectives, goals, assumptions or future events or performance are not statements of historical fact and may be "F0RWARD looking statements."F0RWARD looking statements are based on expectations, estimates and projections at the time the statements are made that involve a number of risks and uncertainties which could cause actual results or events to differ materially from those presently anticipated. F0RWARD looking statements in this action may be identified through the use of words such as "projects", "foresee", "expects", "will," "anticipates," "estimates," "believes," "understands" or that by statements indicating certain actions "may," "could," or "might" occur. As with many microcap stocks, today's company has additional risk factors worth noting. Automotive Capital GR0UP, Inc. is not a reporting company registered under the Securities Act of 1934. Other factors include: an accumulated deficit, a negative net worth, the potential of an increasing public float of stock, a nominal cash position and nominal revenue in its most recent quarter. The company may not be able to continue as a going concern in which case you could lose your entire investment. The publisher of this newsletter does not represent that the information contained in this message states all material facts or does not omit a material fact necessary to make the statements therein not misleading.All information provided within this email pertaining to investing, stocks, securities must be understood as information provided and not investment advice. The publisher of this newsletter advises all readers and subscribers to seek advice from a registered professional securities representative before deciding to trade in stocks featured within this email. None of the material within this report shall be construed as any kind of investment advice or solicitation.Many of these companies are on the verge of bankruptcy. You can lose all your money by investing in this stock. The publisher of The publisher of this newsletter is not a registered investment ADVIS0R. Subscribers should not view information herein as legal, tax, accounting or investment advice. Any reference to past performance(s) of companies are specially selected to be referenced based on the favorable performance of these companies. You would need perfect timing to acheive the results in the examples given. There can be no assurance of that happening. Remember, as always, past performance is nev-er indicative of future results and a thorough due diligence effort, including a review of a company's filings, should be completed prior to investing.The publisher of this newsletter has no relationship with AUML or EMTK. In compliance with the Securities Act of 1933, Section17(b),The publisher of this newsletter discloses the receipt of fifteen thousand dollars from a third party not an officer, director or affiliate shareholder for the circulation of this report. Be aware of an inherent conflict of interest resulting from such compensation due to the fact that this is a paid adver-tisement and is not without bias. All factual information in this report was gathered from public sources, including but not limited to Company Websites and Company Press Releases. The publisher of this newsletter believes this information to be reliable but can make no guar-antee as to its accuracy or completeness. Use of the material within this email constitutes your acceptance of these terms. From fgca at rc.unesp.br Fri Sep 17 12:58:41 2004 From: fgca at rc.unesp.br (Frederico Gonzalez Colombo Arnoldi) Date: Fri Sep 17 12:58:43 2004 Subject: [BioPython] Interfaces for biological programs in python Message-ID: <32989.200.178.59.91.1095440321.squirrel@200.178.59.91> Hi, My name is Frederico Arnoldi and I am studying biology, mainly evolution. I have been writing a graphical interface for alignments in phyton. I am sending this email to ask if Biopython has any interest in it. Thanks Fred From mihran at t-online.de Sat Sep 18 22:51:40 2004 From: mihran at t-online.de (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Sat Sep 18 23:01:39 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogyu7s7/z+8uXw7fvpIPHl?= =?windows-1251?b?8OLo8SDoIOzg8Orl8ujt4yEgIM/w7uTg5uAg7e7z8uHz6u7iIQ==?= Message-ID: <1422828206.20040919025640@> ???????????? ?????? ? ?????????! ??????? ?????????! ????????? ???????????? ??????? Windows'98/2000/NT/XP - ?? 30 ?.?. ?????, ????????? ? ????????? ?????? ???????????? ??????????? - ?? 520 ???. ?? ?????????. ??????????? ????????????? ????? - ?? 15 ?.?. ?? 55 ?.?. (?? 1 ????). ????????? ????? - 650 ??? ? ???. ?????????????? ?????? - ?? 30 ?.? ?? 350 ?.?. ????? ? ??????????? ???? ??????? - ?? 960 ???. ? ???. ??????????? ? ???????? ? ????????? "??? ????" - ?? 940 ???. ??????????? ???????????? 1-3 ?????? ? ???. - ?? 75 ?.?. (????? ? ??????? 2-3 ?????!) ???????? ????????? ???? ? ????? ? ???????????? ????????? ??? ??????????? ???????. ?????? ? ????????? - ?? 150 ?.?. (4 ?????). ???????????????? ?? ?????? ???????-?????????? (???????? ???? ??????????? ? ?????????) - ?? 20 ?.?. ?? 60 ?.?. ???????????????? ?? web - ??????? - ?? 55 ?.?. ?? ???? ??????????? ???????? ???? ? ????????? ????? ????????? (.ru, .su, .com, net, .org, .biz, .info, .edu, .tv, .cc, .ws, .bz, .name, .tm, .aero, coop, .museum, .pro, ? ? ???? .??, .???, .???, .???) - ?? 20 ?.?. ? ???. ?? 1.500.000 ?.?. WEB - ?????? (???????? ??????, ???????? ?? ?????, web - ???????????? ?? ?????, ????????? ???????? ? ???????? ?? ????) - ?? 50 ?.?. ?? 25.000 ?.?. ???????????????? ?? ???????? ???????????? ???????????? - ?? 25 ?.?. ?? 780 ?.?. ???????????? ? ???????? ?? ??????, ?????????, ?????????? - ?? 15 ?.?. ?? 195 ?.?. ????????-?????????, ?????? ???????????? ?????, ???????????????? ?? ????? (??????????? ????????????) - ?? 700 ?.?. ?? 5.900 ? ?????. ??????? ? ????????, ?????????, ???????????, ?????????? ?????? ?? ??? ???? ? ????????? ? ??????????? - ?? 300 ?.?. ?? 1.700 ? ????? ?????? ?? ??????????? ?????? ????? - ?? 200 ?.?. ?? 12.000 ?.?. ??????? ???????? ????? ???????????? ?? ???????????? ???????! ????? ??????? ? ??????? 1 ???! ???????? ? ????????? ? ???????? ???! ???.: (095) 976-9092, 7-888-769 ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From mls5w at virginia.edu Mon Sep 20 16:12:14 2004 From: mls5w at virginia.edu (Michael Sierk) Date: Mon Sep 20 16:08:32 2004 Subject: [BioPython] biopython and compressed PDB files Message-ID: <5D0F78B0-0B41-11D9-B40C-003065C04818@virginia.edu> I was wondering if someone can point me to code that uncompresses PDB files in memory (assuming such a thing is possible)? I found the gzip python module, but apparently that only does .gz files? Thanks, Mike Sierk ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ Michael Sierk, Postdoctoral Fellow email: mls5wvirginiaedu Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 University of Virginia (H): (434) 970-2268 ------------------------------------------------------------------------ ------ "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++ From idoerg at burnham.org Mon Sep 20 16:21:05 2004 From: idoerg at burnham.org (Iddo) Date: Mon Sep 20 16:20:57 2004 Subject: [BioPython] biopython and compressed PDB files In-Reply-To: <5D0F78B0-0B41-11D9-B40C-003065C04818@virginia.edu> References: <5D0F78B0-0B41-11D9-B40C-003065C04818@virginia.edu> Message-ID: <414F3BB1.5020607@burnham.org> Hi Mike, Which version of Python are you using? Python 2.3 has the bz2 module (http://docs.python.org/lib/module-bz2.html). For zip files, there is the zipfile module: http://docs.python.org/lib/module-zipfile.html and the zlib: http://docs.python.org/lib/module-zlib.html#l2h-2626 That should cover it... HTH, ./I Michael Sierk wrote: > I was wondering if someone can point me to code that uncompresses PDB > files in memory (assuming such a thing is possible)? I found the > gzip python module, but apparently that only does .gz files? > > Thanks, > Mike Sierk > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > Michael Sierk, Postdoctoral Fellow email: > mls5wvirginiaedu > Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821 > University of Virginia (H): (434) 970-2268 > ------------------------------------------------------------------------ > ------ > "There is something fascinating about science. One gets such wholesome > returns of conjecture out of such a trifling investment of fact." > -- Mark Twain. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++ > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From aututl at freemail.ch Mon Sep 20 19:08:36 2004 From: aututl at freemail.ch (INFO) Date: Mon Sep 20 19:29:22 2004 Subject: [BioPython] =?iso-8859-1?q?Su=FCer_g=FCnstige_CDs-_Anry?= Message-ID: <4a1201c49f66$c2418190$66471675@aututl> Seid Ihr auf der Suche nach guten, günstigen, gebrauchten und auch ungebrauchten CD´s? Dann habt Ihr nach hoffentlich nicht allzu langer Suche die richtige Adresse gefunden. Das Angebot umfaßt derzeit über 3000 CD´s aus den Richtungen Pop, Rock, Independent, Metal, Deutschrock, Schlager, Techno, Black, und ein wenig Klassik ist ebenfalls vorhanden http://www.jr-cds.de From nomy2020 at yahoo.com Mon Sep 20 22:51:06 2004 From: nomy2020 at yahoo.com (Bzy Bee) Date: Mon Sep 20 22:50:54 2004 Subject: [BioPython] comparing short sequences against genome In-Reply-To: <200409101709.i8AH9DKt029166@portal.open-bio.org> Message-ID: <20040921025106.23818.qmail@web51804.mail.yahoo.com> Hi everyone I want to design 15-20 primers for a differential display experiment on a bacterial genome. The idea is take say 10-15 mer of sequence (from the genome) and compare it against the rest to see how many times it occurs in the genome, followed by next 10 mer and so on. Is there anything in biopython that could help me in doing this? thanks JA __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From dalke at dalkescientific.com Tue Sep 21 05:15:07 2004 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue Sep 21 05:14:40 2004 Subject: [BioPython] EUtils-2.0a1 Message-ID: Hi all, It's been a few months ... okay, more like 4 and I finally have the first alpha version of the new iteration of EUtils done. I won't be able to work on it for the next few days. I hope some of you all here can get a chance to try it out and give me feedback. It's (temporarily) at http://www.dalkescientific.com/EUtils-2.0a1.tar.gz There is essentially no documentation for it. Here are a few examples to get you started. First, the simple interface >>> import EUtils >>> query = EUtils.search("biopython") >>> len(query) 3 >>> for x in query.summary(): ... print x.dataitems["Authors"] ... de Hoon MJ, Imoto S, Nolan J, Miyano S Hamelryck T, Manderick B Mangalam H >>> dbids = EUtils.DBIds("pubmed", ["9390282"]) >>> print EUtils.efetch(dbids, "abstract").read() 1: Pac Symp Biocomput. 1997;:85-96. Using Tcl for molecular visualization and analysis. Dalke A, Schulten K. Beckman Institute, Urbana, IL 61801, USA. Reading and manipulating molecular structure data is a standard task in every molecular visualization and analysis program, but is rarely available in a form readily accessible to the user. Instead, the development of new methods for analysis, display, and interaction is often achieved by writing a new program, rather than building on pre-existing software. We present the Tcl-based script language used in our molecular modeling program, VMD, and show how it can access information about the molecular structure, perform analysis, and graphically display and animate the results. The commands are available to the user and make VMD a useful environment for studying biomolecules. PMID: 9390282 [PubMed - indexed for MEDLINE] >>> One thing to note is the "format" field. This is new. You can ask for formats like "docsum", "brief", "fasta", etc. and it maps the format name to the underlying EUtils request. Eg, "fasta" -> "rettype=fasta&retmode=text" You can force the parameters to be what you want with a new notation, so "fasta/xml" format returns sequence data in the TSeqSet XML format >>> dataset = EUtils.post(EUtils.DBIds("protein", ["12345"])) >>> print dataset.efetch("fasta/xml").read() 12345 CAA44029.1 4565 Triticum aestivum psaI [Triticum aestivum] 36 MTDLNLPSIFVPLVGLVFPAIAMTSLFLYVQKNKIV Here's a new feature. Experimental support for unicode searches. Entrez converts some non-ASCII characters into ASCII by removing accents and other marks. This library tries to support that method. Enable some debugging code >>> from EUtils import ThinClient >>> ThinClient.DUMP_URL = True I'm going to search for a city in Sweden. I originally tried "Espa?a" but it turns out a lot of records had that without the tilde. By comparison, the English spelling of G?teborg is Gothenburg. >>> GOT = u"G\N{LATIN SMALL LETTER O WITH DIAERESIS}teborg" >>> results = EUtils.search(GOT) Opening with GET: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? term=Goteborg&retmax=20&WebEnv=0Y9-O043 -9cLfWBD8rh7CXNDbbccF8wDOOW0fwVKPRkyM890EFVPAe&retstart=0&tool=Biopython _EUtils_2_0&db=pubmed&email=biopython-dev%40biopython.org&usehistory=y See how the term=Goteborg doesn't have any special characters? >>> ThinClient.DUMP_URL = False >>> len(results) 14165 >>> s = results[0].efetch("xml").read() To prove that Goteborg isn't in the string >>> s.find("Goteborg") -1 But that G?teborg is present >>> unicode(s, "utf8").find(GOT) 2594 >>> print unicode(s, "utf8")[2500:2651].encode("utf8") whole communities. Department of Marine Ecology, G?teborg University, Box 461, SE 405 30, G?teborg, Sweden >>> The code I showed above uses a middle layer which is more object oriented. One is DBIdsClient which sends the list of database identifiers to/from the server. The other is the HistoryClient which uses a sort of cookie mechanism at NCBI that lets users store lists of identifiers. I use the HistoryClient for the Entrez searches because that gives access to the list of all matches. By comparison, the DBIdsClient.search takes a count of the maximum number of records to return. Under that is the ThinClient. This does the conversion to the URL requests expected by NCBI. Hopefully it makes some sense even without documentation! WARNING: some of the docstrings are from the version 1 library and haven't been updated to this version 2. Andrew dalke@dalkescientific.com From rlc1 at post.queensu.ca Tue Sep 21 11:11:56 2004 From: rlc1 at post.queensu.ca (Robert Campbell) Date: Tue Sep 21 11:11:40 2004 Subject: [BioPython] biopython and compressed PDB files In-Reply-To: <414F3BB1.5020607@burnham.org> References: <5D0F78B0-0B41-11D9-B40C-003065C04818@virginia.edu> <414F3BB1.5020607@burnham.org> Message-ID: <20040921151156.GA22620@adelie.biochem.queensu.ca> > Michael Sierk wrote: > > >I was wondering if someone can point me to code that uncompresses PDB > >files in memory (assuming such a thing is possible)? I found the > >gzip python module, but apparently that only does .gz files? On 2004-09-20 13:21 Iddo wrote: > > Which version of Python are you using? Python 2.3 has the bz2 module > (http://docs.python.org/lib/module-bz2.html). > > For zip files, there is the zipfile module: > > http://docs.python.org/lib/module-zipfile.html > > and the zlib: > > http://docs.python.org/lib/module-zlib.html#l2h-2626 > > > That should cover it... But actually it doesn't. :( The PDB (for whatever reason) unfortunately uses the UNIX compressed format ".Z" for its files. I'm not sure why as gzip and bzip2 are much better (give better compression) and are more universal. The UNIX Compress program uses the formerly-patented LZW algorithm and so until now there are no ready to use python modules for dealing with .Z files. I haven't found any yet, in any case. See: http://mail.python.org/pipermail/python-list/2004-May/220197.html and http://mail.python.org/pipermail/python-list/2004-May/222565.html So while neither the gzip nor bzip2 python modules can handle a '.Z' file, the system gunzip programs (on Linux) can. So what I'm forced to do is either: os.system("gunzip %s" % compressed_filename) and then read the "filename" or file_as_string = os.popen("gunzip -c %s" % compressed_filename, "r").read() If you are writing something to retrieve pdb files you can use the rcsb web site, rather than the ftp site and specify the compression: filename = urllib.urlretrieve('http://www.rcsb.org/pdb/cgi/export.cgi/' + pdbCode + '.pdb.gz?format=PDB&pdbId=' + pdbCode + '&compression=gz')[0] file_as_string = gzip.GzipFile(filename,'r') Unfortunately for me, I keep my own PDB mirror and "download" from there for speed sake so I'm stuck (for now) "uncompressing". Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 From pjt at 201008247216.user.veloxzone.com.br Tue Sep 21 12:53:04 2004 From: pjt at 201008247216.user.veloxzone.com.br (pjt@201008247216.user.veloxzone.com.br) Date: Tue Sep 21 15:32:16 2004 Subject: [BioPython] Software In-Reply-To: References: Message-ID: software disc ounts and and Adobe Acrobat 6.0 Professional - 100 Games X Copy - 25 Roxio Easy Media Creator 7 - 30 and Adobe Acrobat 6.0 Professional - 100 and AutoCAD Mechanical 2005 DX - 120 DVD Copy Plus - 30 Bryce 5 - 50 Bryce 5 - 50 Macromedia Studio MX 2004 - 180 Microsoft Windows 2000 Professional - 50 Windows 2000 Server - 50 DVD X Maker - 25 Adobe Illustrator 10 - 80 and a lot more http://www.vovowe.biz/ From supportclimax at medusa-art.com Wed Sep 22 19:43:26 2004 From: supportclimax at medusa-art.com (Biopure) Date: Wed Sep 22 18:44:45 2004 Subject: [BioPython] 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 Message-ID: New software on http://www.simpleoem.info/ 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 voyage 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 scalps 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 overseer 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 Maxtor 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 antics 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 Carlisle 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 bulged 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 greed 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 smash 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 Anabaptist 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 excess 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 helping 3D Home Architect Landscape Design Deluxe 6.0 - 29.99 weather http://www.simpleoem.info/ From lounette at celineclub.com Thu Sep 23 04:56:05 2004 From: lounette at celineclub.com (dryden) Date: Thu Sep 23 05:12:05 2004 Subject: [BioPython] =?windows-1251?b?0e/u8PLo4u375SDs6O7x8ujs8+v/8u7w?= =?windows-1251?b?Lfju8PL7IFBPV0VSIEdZTQ==?= Message-ID: <200409230912.i8N9BuKr009831@portal.open-bio.org> ???????????? ??? ?????? ? ??????????? ?????? ??????????? ???? ??????, ???????? ????? ??? ? ?????? ???????? ??????????? ????? ????, ?????? ???????? !!! ?????????? ! ???????? ???????? ???????? 0 ?????? ?? ???? ??????!!! ??????? ??????????? ?? ????? ????????: http://www.pokupki.net From aaron at atroxen.com Wed Sep 22 17:22:25 2004 From: aaron at atroxen.com (Aaron Zschau) Date: Thu Sep 23 10:01:06 2004 Subject: [BioPython] BLAST results and more title information Message-ID: <7F964C98-0CDD-11D9-B329-000A956A65BC@atroxen.com> I'm trying to figure out how to get the full description line from my blast search results I run the following command, where f_record contains a protein string: b_results = NCBIWWW.qblast('blastp', 'nr', f_record, format_type="text") and get a blast file containing the following lines (full file also attached) emb|CAA70306.1| hypoxia-inducible factor one alpha [Mus musculus] 1311 0.0 gb|AAC52730.1| hypoxia-inducible factor 1 alpha 1305 0.0 ref|NP_077335.1| hypoxia inducible factor 1, alpha subunit [Ratt... 1305 0.0 emb|CAA70701.1| hypoxia-inducible factor 1 [Rattus norvegicus] >... 1305 0.0 sp|Q61221|HIFA_MOUSE Hypoxia-inducible factor 1 alpha (HIF-1 alp... 1302 0.0 ref|NP_034561.1| hypoxia inducible factor 1, alpha subunit [Mus ... 1300 0.0 gb|AAH26139.1| Hypoxia inducible factor 1, alpha subunit [Mus mu... 1296 0.0 emb|CAA70305.1| hypoxia-inducible factor one alpha [Mus musculus] 1291 0.0 Is there an easy way to get more information out of the title information instead of being cut off (e.g. getting the full line instead of "hypoxia inducible factor 1, alpha subunit [Mus ... " since some results have longer title lines and sometimes push the species info out of view. thanks, Aaron Zschau -------------- next part -------------- A non-text attachment was scrubbed... Name: 9198.blast Type: application/octet-stream Size: 243750 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040922/1cae2010/9198-0001.obj From dnawi at hotmail.de Thu Sep 23 10:10:54 2004 From: dnawi at hotmail.de (dnawi@hotmail.de) Date: Thu Sep 23 11:21:11 2004 Subject: [BioPython] Whisky direkt nach Hause bestellen Message-ID: <378901c4a177$23cd3e10$25fc7c2e@dnawi> In unserem Online-Shop haben Sie eine reichhaltige Auswahl an feinstem irischen und schottischen Whisk(e)y. Besuchen Sie unsere Internetseite: http://www.whiskyshop24.de From lpritc at scri.sari.ac.uk Thu Sep 23 11:22:35 2004 From: lpritc at scri.sari.ac.uk (Leighton Pritchard) Date: Thu Sep 23 11:22:29 2004 Subject: [BioPython] BLAST results and more title information In-Reply-To: <7F964C98-0CDD-11D9-B329-000A956A65BC@atroxen.com> References: <7F964C98-0CDD-11D9-B329-000A956A65BC@atroxen.com> Message-ID: <4152EA3B.90606@scri.sari.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Aaron, With your BLAST record as b_results, what you're looking for is probably in the b_record.alignments list. Each alignment in b_record.alignments has the full version of the title that is truncated in the summary lines you describe. For example (untested code): |>> b_results = NCBIWWW.qblast('blastp', 'nr', f_record, format_type="text") |>> len(b_results.alignments) # Number of alignments made |>> descriptions = [alignment.title for alignment in b_results.alignments] # Get a list of all descriptions |>> for alignment in b_results.alignments: # Print descriptions, one per line ... print alignment.title might be what you need. L. Aaron Zschau wrote: | I'm trying to figure out how to get the full description line from my | blast search results | | | I run the following command, where f_record contains a protein string: | | b_results = NCBIWWW.qblast('blastp', 'nr', f_record, format_type="text") | | and get a blast file containing the following lines (full file also | attached) | | | emb|CAA70306.1| hypoxia-inducible factor one alpha [Mus musculus] | 1311 0.0 | gb|AAC52730.1| hypoxia-inducible factor 1 alpha | 1305 0.0 | ref|NP_077335.1| hypoxia inducible factor 1, alpha subunit [Ratt... | 1305 0.0 | emb|CAA70701.1| hypoxia-inducible factor 1 [Rattus norvegicus] >... | 1305 0.0 | sp|Q61221|HIFA_MOUSE Hypoxia-inducible factor 1 alpha (HIF-1 alp... | 1302 0.0 | ref|NP_034561.1| hypoxia inducible factor 1, alpha subunit [Mus ... | 1300 0.0 | gb|AAH26139.1| Hypoxia inducible factor 1, alpha subunit [Mus mu... | 1296 0.0 | emb|CAA70305.1| hypoxia-inducible factor one alpha [Mus musculus] | 1291 0.0 | | | Is there an easy way to get more information out of the title | information instead of being cut off (e.g. getting the full line instead | of "hypoxia inducible factor 1, alpha subunit [Mus ... " since some | results have longer title lines and sometimes push the species info out | of view. | | thanks, | | Aaron Zschau | | | | | | ------------------------------------------------------------------------ | | _______________________________________________ | BioPython mailing list - BioPython@biopython.org | http://biopython.org/mailman/listinfo/biopython - -- Dr Leighton Pritchard AMRSC D104, PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK E: lpritc@scri.sari.ac.uk W: http://bioinf.scri.sari.ac.uk/lp/index.shtml T: +44 (0)1382 532761 ext.2405 F: +44 (0)1382 568578 PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFBUuo7L1gZ+OWLpBsRAr8iAJ4mgCLgzVJqSkm/+K1lCHcGF+yz1gCfbPTw RGdqMjGT1KPlV+A6ebFpxTA= =214n -----END PGP SIGNATURE----- From hjm at tacgi.com Fri Sep 24 14:02:38 2004 From: hjm at tacgi.com (Harry Mangalam) Date: Fri Sep 24 14:02:17 2004 Subject: [BioPython] comparing short sequences against genome In-Reply-To: <20040921025106.23818.qmail@web51804.mail.yahoo.com> References: <20040921025106.23818.qmail@web51804.mail.yahoo.com> Message-ID: <200409241102.38080.hjm@tacgi.com> Not biopython per se, but I was just playing around with a short script that does exactly this for oligos from length 2-10. Currently it emits xml for ggobi input, but it would be easy to reformat those statements if you just wanted raw numeric output. It's not a shift/add core so it's not particularly fast (~18s to analyze 8 mers on 140K) and it doesn't deal with degenerate nucs and it's clunky in a number of other ways as well, but you're welcome to plink at it. Because of the way it does bookkeeping, it's memory limited. # seqs x size of hash x # hits, so for large word sizes (>10 or so, it's not well-suited). You'd have to make up your own linked-list-like storage for longer words, I think. OT - I used Numeric.reshape to allocate elements, but afaik, this only allows rectangular arrays. Does python have an easy method for reallocating memory like a ***array in C to handle sparse / non-rectangular arrays? anyway, email if interested. hjm On Monday 20 September 2004 7:51 pm, Bzy Bee wrote: > Hi everyone > > I want to design 15-20 primers for a differential > display experiment on a bacterial genome. The idea is > take say 10-15 mer of sequence (from the genome) and > compare it against the rest to see how many times it > occurs in the genome, followed by next 10 mer and so > on. > > Is there anything in biopython that could help me in > doing this? > > thanks > > JA > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Cheers, Harry Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm@tacgi.com <> From elvira at t-online.de Sat Sep 25 01:50:38 2004 From: elvira at t-online.de (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Sat Sep 25 02:01:10 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogz+vu8uXw7eD/IPDl5+rg?= =?windows-1251?b?ISEhINjl6+ru4/Dg9Oj/ISEhINLo8e3l7ejlISEhINLg7O/u7+X34PL8?= =?windows-1251?q?!!!?= Message-ID: <125258460.20040925055538@> ????????? ?????!!! ???????????!!! ????????!!! ???????????!!! ?????????? ?????: ?????? ???? ??? ???????????: ?? 4?? ??15?? - 9.06 ?.?. ?? ??.?. ?? 15?? ?? 60?? - 6.79 ?.?. ?? ??.?. ?? 60?? ? ????? - 3.69 ?.?. ?? ??.?. ??????? + ????????? ?????? - ?? 15 ?.?. ?? ??.?. ?????????? ??????,???????,?????? ??????????? - ?? 25 ?.?. ??????????? ???????? ????????? ???????????: ??????? ???????? - ?? 1 ?.?. ?? ??. ??. ???????? ????? - ?? 2 ?.?. ?? ??. ??. ????? ?????, ???? ???????????????? ???? ????????? ????????? ??????????? ? ?? ??????? ????: ??????????? ?) ???????? (????????, ?????, ??????, ?????, ???????...). ??????????? ?????? 6?6 M&R "Chameleon" (???, ??????????????????: 3+0, 960 ??????? ??????? ? ?????). ?) ??????????, ??????, ???????, ??????, ??????, ???? (?????? ???????? ? ???, ????????, ????? - ??????, ??????? ?/?...) ?????????????? ?????? Winnon, ??????? ????????? 30?30 ??. ????????. ???????? ??????? (??????, ???????, ????), ?????, ???????. ?? ???????? ?? ????, ???/????: ???????? ?????, ????????, ????????, ????????, ???????????, ?????????, ???. ??????. ??????, ???????: ?????, ????????, ???????, ?????????... ????????????? ?????????????, ???????, ?????????????, ????? -????, ?????? ?????, ????? ??? ?????? ?? ????, ??????? ?? ?????. ???????????. Winnon - 121. ????????? ?? ?????, ?????????, ???????, ??????, ??????????, ????, ???????, ????. ????, ????????????????. ?? ???????? ?????????????? ?????????? ? ? ??????? ??????? ????? ?????? ?? ????????: (095) 7-888-769 (095) 101-3527 (????????.) 8 (926) 523 - 42-41 ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From nomy2020 at yahoo.com Sun Sep 26 22:20:57 2004 From: nomy2020 at yahoo.com (Bzy Bee) Date: Sun Sep 26 22:20:32 2004 Subject: [BioPython] comparing short sequences against genome Message-ID: <20040927022057.26469.qmail@web51802.mail.yahoo.com> Hi BioPython gurus I have been working on this problem of mine, but am stuck and was wondering if someone could help me out here. The following code works on a file with sequences in fasta format (as I can download the exonic sequences in a fasta format). It takes first ten bases of a sequence (as a forward oligo sequence) and then compares it with the rest of sequence, while the 10 mers at a distance of 290 bases are taken as a reverse oligo. It then calculates the gc content and prints the details. What I have been unable to do so far is: 1) the oligos (both forward and reverse) to iterate through the entire file, i.e. each and every sequence in the file (and keeping track of sequence names and positions when a match is found). At the moment it just takes the first 10 mers of sequence 1 (and 10 mers at position 290) and compares these with sequence 1, but not with sequence 2 and 3 and so on 2) secondly, I want to add one to the starting position of 10 mers, i.e. in the second round of iteration, instead of taking: oligoF = result[0:10] it should take result[1:11], i.e. increasing the position of 10 mer by 1 (and same for reverse oligo) and so on until teh sequence finishes. I'm not sure how to increment the result by 1. I am kinda stuck at both these steps and any help would be very much appreciated. Here's my code: ============================================= from string import * import string from Bio.SeqIO import FASTA def findOlig(dna, prim): ''' This method finds all the occurences of a short 10 mer in a sequence''' loc = [] count = 0 site = dna.find(prim) while site != -1: loc.append(site) site = dna.find(prim, site + 1) count += 1 print 'primer sequence: ', prim, 'no of times present:', count, 'oligo site:', loc def revComp(dna): ''' This method is used to get the reverse complement of a sequence''' comp = dna.translate(maketrans("AGCTagct", "TCGAtcga")) lcomp = list(comp) lcomp.reverse() return join(lcomp, '') def gcContent(dna): '''This method finds gc percent of a given sequence ''' length = len(dna) count_gc = count(dna, 'g') + count(dna, 'G') + count(dna, 'c') + count(dna, 'C') gc = float(count_gc)/length *100 return gc # read the fasta file and find the oligos (and print their details) in the sequences handle = open('some_file.txt') it = FASTA.FastaReader(handle) #seq = it.next() while 1: seq = it.next() if seq is None: break result = string.join(myseq.seq, '') oligoF = result[0:10] oligoR = result[290:300] findOlig(result, oligoF) findOlig(result, oligoR) print oligoF, "GC content:", gcContent(oligoF) print revComp(oligoR), "GC content:", gcContent(oligoR) print myseq.name print result handle.close() =========================================== where some_file.txt has: >Seq1 There is some description here ATGAATCCAAGCCAAATACTTGAAAATTTAAAAAAAGAATTAAGTGAAAACGAATACGAAAACTATTTATCAAATTTAAAATTCAACGAAAAACAAAGCAAAGCAGATCTTTTAGTTTTTAATGCTCCAAATGAACTCATGGCTAAATTCATACAAACAAAATACGGCAAAAAAATCGCGCATTTTTATGAAGTGCAAAGCGGAAATAAAGCCATCATAAATATACAAGCACAAAGTGCTAAACAAAGCAACAAAAGCACAAAAATCGACATAGCTCATATAAAAGCACAAAGCACGATTTTAAATCCTTCTTTTACTTTTGAAAGTTTTGTTGTAGGGGATTCTAACAAATACGCTTATGGAGCATGTAAAGCCATAGCACATAAAGACAAACTTGGAAAACTTTATAATCCAATCTTTGTTTATGGACCTACAGGACTTGGAAAAACACATTTACTTCAAGCAGTTGGAAATGCAAGCTTAGAAATGGGAAAAAAAGTTATTTACGCTACCAGTGAAAATTTCATCAACGATTTTACTTCAAATTTAAAAAATGGTTCTTTAGATAAATTTCATGAAAAGTATAGAAACTGCGATGTTTTACTTATAGATGATGTACAGTTTTTAGGAAAAACCGATAAAATTCAAGAAGAATTTTTCTTTATATTTAATGAAATCAAAAATAACGATGGACAAATCATCATGACTTCAGACAATCCACCCAACATGCTAAAAGGTATAACCGAACGCTTAAAAAGTCGTTTTGCACATGGGATCATAGCTGATATAACTCCACCTCAACTAGATACAAAAATAGCCATCATAAGAAAAAAATGTGAATTTAACGATATCAATCTTTCTAATGATATTATAAACTATATCGCTACTTCTTTAGGGGATAATATAAGAGAAATCGAAGGTATCATCATAAGTTTAAATGCTTATGCAACCATACTAGGACAAGAAATCACACTCGAACTTGCCAAAAGTGTGATGAA AGATCATATCAAAGAAAAGAAAGAAAATATCACTATAGATGACATTTTATCTTTGGTATGTAAAGAATTTAACATCAAACCAAGCGATGTGAAATCCAATAAAAAAACTCAAAATATAGTCACAGCAAGACGCATTGTGATTTACCTAGCTAGGGCACTTACGGCTTTGACTATGCCACAACTTGCGAATTATTTTGAAATGAAAGATCATACAGCTATTTCACATAATGTTAAAAAAATCACAGAAATGATAGAAAATGATGCTTCTTTAAAAGCAAAAATCGAAGAACTTAAAAACAAAATTCTTGTTAAAAGTCAAAGTTAA >seq2 There is some description here ATGAAGTTAAGTATCAATAAAAATACTTTAGAATCTGCAGTGATTTTATGTAATGCTTATGTAGAAAAAAAAGACTCAAGCACCATTACTTCTCATCTTTTTTTTCATGCTGATGAAGATAAACTTCTTATTAAAGCTAGTGATTATGAAATAGGTATCAACTATAAAATAAAAAAAATCCGCGTAGAATCAAGTGGTTTTGCTACTGCAAATGCAAAAAGTATTGCAGATGTTATTAAAAGCTTAAACAATGAAGAAGTTGTTTTAGAAACCATTGATAATTTTTTATTTGTAAGACAAAAAAGTACAAAATACAAACTTCCTATGTTTAATCATGAAGATTTTCCAAATTTTCCAAATACAGAAGGAAAAAACCAATTTGACATTGATTCAAGTGATTTAAGCCGTTCTCTTAAAAAGATATTACCAAGTATTGATACAAATAACCCAAAATACTCCTTAAATGGTGCATTTTTAGATATAAAAACAGATAAAATTAACTTCGTAGGAACTGATACAAAACGCCTTGCAATCTATACTTTAGAAAAAGCAAATAATCAAGAATTTAGTTTTAGTATCCCTAAAAAAGCTATTATGGAAATGCAAAAACTTTTCTATGAAAAAATAGAAATTTTTTATGATCAAAATATGCTTATTGCCAAAAATGAAAATTTTGAATTCTTTACAAAACTTATCAATGATAAATTTCCAGATTATGAAAAAGTTATACCAAAAACTTTCAAACAAGAACTCAGTTTTTCAACTGAAGATTTTATAGATAGTCTTAAAAAAATCAGCGTTGTAACTGAAAAAATGAGACTTCATTTTAACAAAGATAAAATCATCTTTGAAGGTATAAGTTTAGACAATATGGAAGCAAAAACAGAACTTGAAATTCAAACAGGAGTAAGTGAAGAATTTAATCTTACTATAAAAATCAAACATTTACTTGATTTCTTAACTTCTATAGAAGAAGAAAAATTCACTTTAAGTGTAAA TGAACCTAATTCAGCATTTATAGTCAAATCCCAAGGACTATCAATGATTATCATGCCTATGATTTTGTAA Thanks a lot for your help regards J Ali --- Bzy Bee wrote: > Subject: Re: [BioPython] comparing short sequences > against genome > Date: Mon, 20 Sep 2004 > Hi everyone > > I want to design 15-20 primers for a differential > display experiment on a bacterial genome. The idea > is take say 10-15 mer of sequence (from the genome) > and compare it against the rest to see how many > times it occurs in the genome, followed by next 10 > mer and so on. > > Is there anything in biopython that could help me > in doing this? > > thanks > > JA > > Do You Yahoo!? __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From nomy2020 at yahoo.com Sun Sep 26 22:20:57 2004 From: nomy2020 at yahoo.com (Bzy Bee) Date: Sun Sep 26 22:20:33 2004 Subject: [BioPython] comparing short sequences against genome Message-ID: <20040927022057.26469.qmail@web51802.mail.yahoo.com> Hi BioPython gurus I have been working on this problem of mine, but am stuck and was wondering if someone could help me out here. The following code works on a file with sequences in fasta format (as I can download the exonic sequences in a fasta format). It takes first ten bases of a sequence (as a forward oligo sequence) and then compares it with the rest of sequence, while the 10 mers at a distance of 290 bases are taken as a reverse oligo. It then calculates the gc content and prints the details. What I have been unable to do so far is: 1) the oligos (both forward and reverse) to iterate through the entire file, i.e. each and every sequence in the file (and keeping track of sequence names and positions when a match is found). At the moment it just takes the first 10 mers of sequence 1 (and 10 mers at position 290) and compares these with sequence 1, but not with sequence 2 and 3 and so on 2) secondly, I want to add one to the starting position of 10 mers, i.e. in the second round of iteration, instead of taking: oligoF = result[0:10] it should take result[1:11], i.e. increasing the position of 10 mer by 1 (and same for reverse oligo) and so on until teh sequence finishes. I'm not sure how to increment the result by 1. I am kinda stuck at both these steps and any help would be very much appreciated. Here's my code: ============================================= from string import * import string from Bio.SeqIO import FASTA def findOlig(dna, prim): ''' This method finds all the occurences of a short 10 mer in a sequence''' loc = [] count = 0 site = dna.find(prim) while site != -1: loc.append(site) site = dna.find(prim, site + 1) count += 1 print 'primer sequence: ', prim, 'no of times present:', count, 'oligo site:', loc def revComp(dna): ''' This method is used to get the reverse complement of a sequence''' comp = dna.translate(maketrans("AGCTagct", "TCGAtcga")) lcomp = list(comp) lcomp.reverse() return join(lcomp, '') def gcContent(dna): '''This method finds gc percent of a given sequence ''' length = len(dna) count_gc = count(dna, 'g') + count(dna, 'G') + count(dna, 'c') + count(dna, 'C') gc = float(count_gc)/length *100 return gc # read the fasta file and find the oligos (and print their details) in the sequences handle = open('some_file.txt') it = FASTA.FastaReader(handle) #seq = it.next() while 1: seq = it.next() if seq is None: break result = string.join(myseq.seq, '') oligoF = result[0:10] oligoR = result[290:300] findOlig(result, oligoF) findOlig(result, oligoR) print oligoF, "GC content:", gcContent(oligoF) print revComp(oligoR), "GC content:", gcContent(oligoR) print myseq.name print result handle.close() =========================================== where some_file.txt has: >Seq1 There is some description here ATGAATCCAAGCCAAATACTTGAAAATTTAAAAAAAGAATTAAGTGAAAACGAATACGAAAACTATTTATCAAATTTAAAATTCAACGAAAAACAAAGCAAAGCAGATCTTTTAGTTTTTAATGCTCCAAATGAACTCATGGCTAAATTCATACAAACAAAATACGGCAAAAAAATCGCGCATTTTTATGAAGTGCAAAGCGGAAATAAAGCCATCATAAATATACAAGCACAAAGTGCTAAACAAAGCAACAAAAGCACAAAAATCGACATAGCTCATATAAAAGCACAAAGCACGATTTTAAATCCTTCTTTTACTTTTGAAAGTTTTGTTGTAGGGGATTCTAACAAATACGCTTATGGAGCATGTAAAGCCATAGCACATAAAGACAAACTTGGAAAACTTTATAATCCAATCTTTGTTTATGGACCTACAGGACTTGGAAAAACACATTTACTTCAAGCAGTTGGAAATGCAAGCTTAGAAATGGGAAAAAAAGTTATTTACGCTACCAGTGAAAATTTCATCAACGATTTTACTTCAAATTTAAAAAATGGTTCTTTAGATAAATTTCATGAAAAGTATAGAAACTGCGATGTTTTACTTATAGATGATGTACAGTTTTTAGGAAAAACCGATAAAATTCAAGAAGAATTTTTCTTTATATTTAATGAAATCAAAAATAACGATGGACAAATCATCATGACTTCAGACAATCCACCCAACATGCTAAAAGGTATAACCGAACGCTTAAAAAGTCGTTTTGCACATGGGATCATAGCTGATATAACTCCACCTCAACTAGATACAAAAATAGCCATCATAAGAAAAAAATGTGAATTTAACGATATCAATCTTTCTAATGATATTATAAACTATATCGCTACTTCTTTAGGGGATAATATAAGAGAAATCGAAGGTATCATCATAAGTTTAAATGCTTATGCAACCATACTAGGACAAGAAATCACACTCGAACTTGCCAAAAGTGTGATGAA AGATCATATCAAAGAAAAGAAAGAAAATATCACTATAGATGACATTTTATCTTTGGTATGTAAAGAATTTAACATCAAACCAAGCGATGTGAAATCCAATAAAAAAACTCAAAATATAGTCACAGCAAGACGCATTGTGATTTACCTAGCTAGGGCACTTACGGCTTTGACTATGCCACAACTTGCGAATTATTTTGAAATGAAAGATCATACAGCTATTTCACATAATGTTAAAAAAATCACAGAAATGATAGAAAATGATGCTTCTTTAAAAGCAAAAATCGAAGAACTTAAAAACAAAATTCTTGTTAAAAGTCAAAGTTAA >seq2 There is some description here ATGAAGTTAAGTATCAATAAAAATACTTTAGAATCTGCAGTGATTTTATGTAATGCTTATGTAGAAAAAAAAGACTCAAGCACCATTACTTCTCATCTTTTTTTTCATGCTGATGAAGATAAACTTCTTATTAAAGCTAGTGATTATGAAATAGGTATCAACTATAAAATAAAAAAAATCCGCGTAGAATCAAGTGGTTTTGCTACTGCAAATGCAAAAAGTATTGCAGATGTTATTAAAAGCTTAAACAATGAAGAAGTTGTTTTAGAAACCATTGATAATTTTTTATTTGTAAGACAAAAAAGTACAAAATACAAACTTCCTATGTTTAATCATGAAGATTTTCCAAATTTTCCAAATACAGAAGGAAAAAACCAATTTGACATTGATTCAAGTGATTTAAGCCGTTCTCTTAAAAAGATATTACCAAGTATTGATACAAATAACCCAAAATACTCCTTAAATGGTGCATTTTTAGATATAAAAACAGATAAAATTAACTTCGTAGGAACTGATACAAAACGCCTTGCAATCTATACTTTAGAAAAAGCAAATAATCAAGAATTTAGTTTTAGTATCCCTAAAAAAGCTATTATGGAAATGCAAAAACTTTTCTATGAAAAAATAGAAATTTTTTATGATCAAAATATGCTTATTGCCAAAAATGAAAATTTTGAATTCTTTACAAAACTTATCAATGATAAATTTCCAGATTATGAAAAAGTTATACCAAAAACTTTCAAACAAGAACTCAGTTTTTCAACTGAAGATTTTATAGATAGTCTTAAAAAAATCAGCGTTGTAACTGAAAAAATGAGACTTCATTTTAACAAAGATAAAATCATCTTTGAAGGTATAAGTTTAGACAATATGGAAGCAAAAACAGAACTTGAAATTCAAACAGGAGTAAGTGAAGAATTTAATCTTACTATAAAAATCAAACATTTACTTGATTTCTTAACTTCTATAGAAGAAGAAAAATTCACTTTAAGTGTAAA TGAACCTAATTCAGCATTTATAGTCAAATCCCAAGGACTATCAATGATTATCATGCCTATGATTTTGTAA Thanks a lot for your help regards J Ali --- Bzy Bee wrote: > Subject: Re: [BioPython] comparing short sequences > against genome > Date: Mon, 20 Sep 2004 > Hi everyone > > I want to design 15-20 primers for a differential > display experiment on a bacterial genome. The idea > is take say 10-15 mer of sequence (from the genome) > and compare it against the rest to see how many > times it occurs in the genome, followed by next 10 > mer and so on. > > Is there anything in biopython that could help me > in doing this? > > thanks > > JA > > Do You Yahoo!? __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From =?iso-2022-jp?Q?3=1B=24B2/1=5F!=22=1B=28B5=1B=24B2/1=5F=3EZ5r=1B=28B?= Mon Sep 27 05:33:59 2004 From: =?iso-2022-jp?Q?3=1B=24B2/1=5F!=22=1B=28B5=1B=24B2/1=5F=3EZ5r=1B=28B?= (=?iso-2022-jp?Q?3=1B=24B2/1=5F!=22=1B=28B5=1B=24B2/1=5F=3EZ5r=1B=28B?=) Date: Mon Sep 27 05:36:02 2004 Subject: [BioPython] =?iso-2022-jp?b?GyRCIXZMJD41QnohdT41Qno5LTlwIiMbKEI=?= =?iso-2022-jp?b?GyRCIzMyLzFfISIjNTIvMV9FeSROPH1GfjxUQjM9UCEmPlo1ciRHGyhC?= =?iso-2022-jp?b?GyRCPVBNaCRrIiNHLzZiJE8bKEI4GyRCQGlLfDFfQ3k2YiRHSVQbKEI=?= =?iso-2022-jp?b?GyRCTVciIzdKNSQyc0l8Mys7TyROO34kMyQ9JUElYyVzJTkhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= Message-ID: <5527570.1096277639037.JavaMail.nobody@hosyou-b.mine.nu> biopython@biopython.org$BMM(B $B!!(B $B!!!!7P:QJ88K!!%a%k%^%,C4EvLpBt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $Bl9g$O$=$N;]$r(B http://gogoway.pimpdomain.com/melmaga/teishi.html$B$^$G(B $B!!!!!!!!!!(B $B%a!<%k%^%,%8%s9-9p?=$79~$_$O!"$=$N;]$r!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm$B$^$G(B $B!!!!!!!!!!!!(B $B%a!<%k%^%,%8%s9XFI$N?=$79~$N>l9g$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/melmaga/$B$^$G(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!(B--$B#6@iK|1_$G4jK>$OC#@.!!(B----$B!!J}K!$O$"$j$^$9!*!!(B------$B!!#6@iK|1_0J2e$NCK=w$J$i=PMh$k![(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B:#$NG:$_$O!&!&!@iK|1_$G2r7h=PMh$k!*L\E*$K$b;HMQ=PMh$k!*@83h8~>e=PMh$k(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B>-Mh$NIT0B$O!&!&!@iK|1_Cy6b$G0B?4=PMh$k!*0B?48~>e$N:`NA$O;q6b$G=PMh$k!*(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B=PMh$k$NJ}K!$OM-$j$^$9!#(B $B"!(,!N#P#R!O(,(,7J5$$O5^2sI|3+;O$7$^$7$?(,"#(B $B#22/1_!"(B $B#32/1_!"(B $B#52/#9@iK|1_<}F~Z5rM-<}F~%S%8%M%9!U7P1DeCK=w?=$79~$_=PMh$^$9!#(B $B!!!!!!I{6H!&7s6H!&EZF|7P1D2K3hMQ7P1D$NJ}!9$KBg9%I>!*(B $B!!!!!!!!(B $B!!!!!!!!#3#8G/$N\$7$/$O(B http://gogoway.pimpdomain.com$B!!(B $B!!!!!!!!!!!!2?;v$bO@$h$j>Z5r!&1=$h$j>Z5r!&>u67>Z5r$h$jJ*E*>Z5r!&:[H=41$HF1$8J*E*>Z5r$N$_$G;ve$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o(^$B"&(B^)o$B=i$a$F$NI{<}F~$OMb7n$K$b$i$($?$o(B(*^-$B!,(B)v $B!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B *-----$B#P#R(B------------------------------------------------------------------------------------------------* $B#87n%W%l%*!<%W%sFCJL1o8NJg=8$N30;q7O%M%C%H%o!<%/4k6H$N0lHL8xJgOH(B $B!!!!!!!!!!(B $B!!(B http://askmebiz.net/click/2/ad5.cgi $B!z!y(B $B!2#P#R!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z(B $B!!(B $B1?L?$rJQ$($k%o%s%/%j%C%/$bM-$j$^$9!#!!FCJL5.IP@J!!;D$j$o$:$+(B *-------------------------------------------------------* $B!z(Bo(^$B"`(B^o) $BKhF|$,%a%C%A%c3Z$7$$$s$G$9$%$%!7W;;5!!"9bB.%3%$%s%+%&%s%?!l!W!"!VBgGW:V!W$,$"$J$?$N7HBS$GM7$Y$^$9!*(B $B!!!!!!!!!!!J(BBREW$B!"(BVodafone$BBP1~!K(B $B#1%"%W%j!o#1#5#7!A$G$9$N$G!"$*;E;v$N9g4V$N$A$g$C$H$7$?B)H4$-$K(B $B!!$*5$7Z$K@'Hs$4MxMQ2<$5$$"v(B http://www.metro-japan.com/mobile/index.html $B!z(B--$B!~(B-$B!N(BPR]-$B!z(B--$B"!(B--$B!z(B--$B!~(B--$B!z!z(B-$B!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B-$B!~(B--$B!z(B--$B"!(B--$B!z=i$a$F$NI{<}F~$OMb7n(B--$B!~(B-$B!z(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B!!(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v$@$C$Fe$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o $B!!!!!!!!!!!!!!!!!!!!!!!!!!!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B $B!!!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B *:$B!z(B $B!!!!!}!!K\F|$bEj9F!*$"$j$,$H$&$4$6$$$^$7$?"v!}%a%k%^%,H/9TpJspJs$K4X$7$FH/9T5$/$@$5$$!#7G:\5-;v$K4X$9$k$*Ld$$9g$o$;$OD>@\Ej9Fl9g$O5$/$@$5$$!#(B $B!!!!!!!!!!!!$^$?9-9pFbMF$K$h$C$F$O!!7G:\$r95$($5$;$F$$$?$@$/>l9g$b$4$6$$$^$9!#(B $B!!!!!!!!!!!!9-9p$r?=$79~$s$G$$$?$@$$$?J}$K$O!"%a!<%k%^%,%8%s$rG[?.$5$;$F$$$?$@$-$^$9!#(B $B!!!!!!!!!!!!$4N;>5$N>e!!$*?=$79~$_$/$@$5$$!#(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm ---------------------------------------------------------- $B!!!!!!!!!!!!!!!!!!!!!!(B $B%a!<%k%^%,%8%s!!9-9pC4EvLpBt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!(B ------------------------------------------- 9$B7n(B27$BF|(B5$B;~H/I=(B $B8E20(B $BF^$j0l;~1+(B $BF^$j$N$A0l;~1+(B $B?73c(B $BF^$j(B $BF^$j$N$A;~!9@2$l(B $B6bBt(B $B1+$N$AF^$j(B $BF^$j(B $BBg:e(B $B1+$N$AF^$j(B $BF^$j$N$A0l;~1+(B $B2,;3(B $B1+$N$AF^$j(B $BF^$j$N$A0l;~1+(B $B9-Eg(B $B1+$N$AF^$j(B $BF^$j$N$A0l;~1+(B $B9b>>(B $BF^$j(B $BF^$j$N$A0l;~1+(B $BJ!2,(B $B1+$N$AF^$j(B $BF^$j$N$A0l;~1+(B $B This is actually a Numeric python error, but as I ran across in the installation of BioPython I thought others might have experience of this error. While doing the dependency dance necessary to get a fresh installation of BioPython running (the box is a Xeon processor running SUSE) the install barfs at the point it generates the lapack library: gcc -pthread -shared build/temp.linux-i686-2.3/Src/lapack_litemodule.o -L/usr/lib/atlas -llapack -lcblas -lf77blas -latlas -lg2c -o build/lib.linux-i686-2.3/lapack_lite.so /usr/lib/gcc-lib/i586-suse-linux/3.3.3/../../../../i586-suse-linux/bin/ ld: cannot find -llapack collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1 And just BTW, any idea of when Biopython might move from Numeric to Numarray? -- Dr Paul-Michael Agapow (p.agapow@ucl.ac.uk) Dept. Biology, University College London From bartek at rezolwenta.eu.org Mon Sep 27 20:30:00 2004 From: bartek at rezolwenta.eu.org (bartek wilczynski) Date: Mon Sep 27 20:51:32 2004 Subject: [BioPython] comparing short sequences against genome In-Reply-To: <20040927022057.26469.qmail@web51802.mail.yahoo.com> References: <20040927022057.26469.qmail@web51802.mail.yahoo.com> Message-ID: <1096331400.4158b088afaf6@imp.rezolwenta.eu.org> Citing Bzy Bee : > What I have been unable to do so far is: > > 1) the oligos (both forward and reverse) to iterate > through the entire file, i.e. each and every sequence > in the file (and keeping track of sequence names and > positions when a match is found). At the moment it > just takes the first 10 mers of sequence 1 (and 10 > mers at position 290) and compares these with sequence > 1, but not with sequence 2 and 3 and so on > > 2) secondly, I want to add one to the starting > position of 10 mers, i.e. in the second round of > iteration, instead of taking: > oligoF = result[0:10] > it should take result[1:11], i.e. increasing the > position of 10 mer by 1 (and same for reverse oligo) > and so on until teh sequence finishes. I'm not sure > how to increment the result by 1. > > I am kinda stuck at both these steps and any help > would be very much appreciated. Hi, I've attached modified version of your program that does what you want. It's not clean and it's not even nearly as fast as it needs to be if you are thinking about genomic scale experiments. If you need to just do this once and not for very long sequences, you can use this. Otherwise, I would recommend reading something about suffix trees. HOnestly I don't know if there's any code related to that in biopython. regards Bartek Wilczynski -------------- next part -------------- A non-text attachment was scrubbed... Name: fasta_compare.py Type: text/x-python Size: 2219 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040928/af68a067/fasta_compare.py From mdehoon at ims.u-tokyo.ac.jp Mon Sep 27 22:09:28 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Mon Sep 27 22:06:52 2004 Subject: [BioPython] LAPACK error In-Reply-To: <56D07AF4-10C7-11D9-A984-000A95D1E3BA@agapow.net> References: <56D07AF4-10C7-11D9-A984-000A95D1E3BA@agapow.net> Message-ID: <4158C7D8.4090601@ims.u-tokyo.ac.jp> > And just BTW, any idea of when Biopython might move from Numeric to > Numarray? I am not sure to what degree numarray has been accepted by the user community as a replacement for Numeric. For example, SciPy expects this transition to take years. The transition will not be that straightforward either, as some of the C extension modules will have to be modified. So my personal expectation is that it may take some time. What do other users/developers think? Paul-Michael Agapow wrote: > gcc -pthread -shared build/temp.linux-i686-2.3/Src/lapack_litemodule.o > -L/usr/lib/atlas -llapack -lcblas -lf77blas -latlas -lg2c -o > build/lib.linux-i686-2.3/lapack_lite.so > /usr/lib/gcc-lib/i586-suse-linux/3.3.3/../../../../i586-suse-linux/bin/ > ld: cannot find -llapack > collect2: ld returned 1 exit status > error: command 'gcc' failed with exit status 1 I have seen this error before, but only with the latest version of Numeric (23.3). With to the earlier version (23.1) of Numeric, I had no such problems. So that might be your easiest solution. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From agnes at eurotelecom.ru Tue Sep 28 11:42:42 2004 From: agnes at eurotelecom.ru (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Tue Sep 28 11:50:11 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4DogxOjn4OntISEh?= Message-ID: <187191165.20040928154742@> ????????? ?????! ???????! ???????? ????? ???????? ??? ???????????, ?????? ?/??? ??????. ? ?????????? ????????? ??????. ?????????? ????????, ?????????? ????? - ?? 450 ?.?. ?? ... ?? 15 ?.?. ?? ????? ????????? ????????? ?? 2500 ?.?. ?? ?????????? ????????? ????????, ???????, ????? - ????. ??????-???? (????????? ???????? ?? ???? ?? ??????) ?? 500 ?.?. ???????? ? ??????? ???????????? ???????????????, Corbis, Fotobank ? ???????. ?? ?????????? ? ???????????? ???? - ???????! ??????????? ?????? ????? ? ????? ?????????????! ????????? ??? ????? ??????! ? ??? ????????? ??????? ??? ???????????! ???.: (095) 101-3527 ??????????, ?? ????????? ????? ?? ???????? ?????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From mec at stowers-institute.org Tue Sep 28 16:21:48 2004 From: mec at stowers-institute.org (Malcolm Cook) Date: Tue Sep 28 16:30:39 2004 Subject: [BioPython] comparing short sequences against genome References: <20040927022057.26469.qmail@web51802.mail.yahoo.com> <1096331400.4158b088afaf6@imp.rezolwenta.eu.org> Message-ID: and look at ssaha and blat (which has bioperl wrapper) "bartek wilczynski" wrote in message news:1096331400.4158b088afaf6@imp.rezolwenta.eu.org... > Citing Bzy Bee : > > > What I have been unable to do so far is: > > > > 1) the oligos (both forward and reverse) to iterate > > through the entire file, i.e. each and every sequence > > in the file (and keeping track of sequence names and > > positions when a match is found). At the moment it > > just takes the first 10 mers of sequence 1 (and 10 > > mers at position 290) and compares these with sequence > > 1, but not with sequence 2 and 3 and so on > > > > 2) secondly, I want to add one to the starting > > position of 10 mers, i.e. in the second round of > > iteration, instead of taking: > > oligoF = result[0:10] > > it should take result[1:11], i.e. increasing the > > position of 10 mer by 1 (and same for reverse oligo) > > and so on until teh sequence finishes. I'm not sure > > how to increment the result by 1. > > > > I am kinda stuck at both these steps and any help > > would be very much appreciated. > > > Hi, > > I've attached modified version of your program that does what you want. It's not > clean and it's not even nearly as fast as it needs to be if you are thinking > about genomic scale experiments. > > If you need to just do this once and not for very long sequences, you can use > this. Otherwise, I would recommend reading something about suffix trees. > HOnestly I don't know if there's any code related to that in biopython. > > regards > > Bartek Wilczynski > ---------------------------------------------------------------------------- ---- > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From biopython-dev-bounces at portal.open-bio.org Tue Sep 28 19:14:34 2004 From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org) Date: Tue Sep 28 19:14:36 2004 Subject: [BioPython] Your message to Biopython-dev awaits moderator approval Message-ID: Your mail to 'Biopython-dev' with the subject Re: Is being held until the list moderator can review it for approval. The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/2dbc09383858aaf2a3d591886a81748a2560af4f From brian at eurotelecom.ru Wed Sep 29 03:40:39 2004 From: brian at eurotelecom.ru (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Wed Sep 29 03:43:42 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogz+7i+/jl7ejlIPHv8O7x?= =?windows-1251?b?4Cwg4vvx8uDi6ughISE=?= Message-ID: <1255633693.20040929074539@> ???????? ?????!!! ????????, ??????????, ?????????????, ?????????? ???????? ????? ????? ????? ???????????? ? ?????? ?????????! ?????????? ??????, ??????????? ? ???????? ? ???????????! ???????? ? ?????? ?????????? ?????????! ??????? ???????????? ????! ???????????????? ??????????! ?????????? ?????? ? ????????????! ???? ?????? ???????? - ??????-????? - ? ????? ???????!!! ???? ?????????! 1. ?????? ?????. "????-?????". ?????????? ????????, ?????????? ????? - ?? 450 ?.?. ?? ... ?? 15 ?.?. ?? ????? ????????? ????????? ?? 2500 ?.?. ?? ?????????? ????????? ????????, ???????, ????? - ????. ??????-???? (????????? ???????? ?? ???? ?? ??????) ?? 500 ?.?. ???????? ? ??????? ???????????? ???????????????, Corbis, Fotobank ? ???????. ?? ?????????? ? ???????????? ???? - ???????! ??????????? ?????? ????? ? ????? ?????????? ?? ?????? ? ?????????! 2. ????????. 30.000 ?????????. 190 ?????????! ??????? ????????: 1. ??????-???????, 200 ??., 1 + 0 - 263 ?.?. 2. ?????, ??????, ???????, 1000 ??. - 0,54 ?.?. 3. ?????????, ???, + ?????, 50 ??. - 11,24 ?.?. 4. ????????? ?????????, ????, 100??. - 11,5 ?.?. ?/?, 100??. - 5,60 ?.?. 5. ??????, ????????, ?????, 200 ??, 50 ??. - 1,95 ?.?. 6. ??????,240??, 50 ??. - 19,95 ?.?. 7. ?????-?????,??????-??????,350 ?? - ?? 28 ?.?. 8. ????-?????????, ???????, 50 ??. - 9,30 ?.?. 8. ????-?????????, ??????, 50 ??. - 15,08 ?.?. 9. ?????, ??????, ? ???????, 20 ??. - 13,5 ?.?. 10. ?????, ???????,50 ??. - 8,5 ?.?. 11. ???????? ??? ????, ??????, 20 ??. - 4,10 ?.?. 12. ????? ??????????, ???? - 10,7 ?.?. 13. ??????, 6?3,5??, 4 + 4, 1000 ??. - 0,87 ?.?. 14. ???? ?????????,50 ??. - 8,10 ?.?. 15. ????????? - ????, ??????, 50 ??.- 4,10 ?.?. 16. ?????????, ???????, ?????, 100 ??. - 0,51 ?.?. 17. ???????, ?4, 50 ??????, ???????, 2 + 0, 100 ??. - 2,80 ?.?. 18. ?????? ?????, 4 ???????? - 14,60 ?.?. 19. ?????? ??? ????, 500 ??, 1 + 0, ??????, 200 ??. - 6,29 ?.?. 20. ?????, 2 + 0, 192 ??. - 359 ?.?. 21. ???????, 100 ??., 3+0 - 426 ?.?. 22. ?????????, ?????, ? ??????????, 200 ??. - 6,4 ?.?. 23. ????? ????????? + ?????, 50 ??. - 11,24 ?.?. 24. ????? ????????? + ????? + ??????, 50 ??. - 12,3 ?.?. 25. ??????? ?????????? ?????, ?????, 50 ??. - 24 ?.?. 26. ???? ??????, Doppler (???????), 1 + 0, 100 ??. - 860 ?.?. 27. ?????????? ??????, 9?15 ??, ???? - 10,7 ?.?. ???????? ??-?? ?????????, ?????, ????????, ??????, ??????, ??????! ????????? ???????? ??? ?????????, ????????? 140 ?/??.?.: ?? 10 ?? 100 ??. - 2,3 ?.?., 150 ?/??.?., ?? 500 ?? 1000 ??. - 2,2 ?.?., 160 ?/??.?., ?? 100 ?? 500 ?? - 2,5 ?.?., ?? 1000 ?? 5000 ??. - 2,2 ?.?. ?????? ?? ? ??????????,1+0: 100 ??. - 60 ?.?., 1000 ??. - 190 ?.?., 5000 ??. - 580 ?.?., ?? ??????? ???????? ???????, ???????? ????????? ?????? ?????? ?????, 50 ???, ? ????????? ????????? ??????. ???????? ? ??????????,?65, ???????, 1+0: 500 ?? - 110 ?.?., 5000 ??.- 480 ?.?., ?????. ????. ???????? ??????? ?? ????: ?????????????, ?????? 9,5 ? 6,5 ?? - 5 ?.?. ???????, ?????? 16 ? 12 ?? - 11 ?.?. ????? ??? ?????? ??????? ?5 - ?? 20 ?.?. ????? ????, ????? ??? ????? ??????? ?4 - ?? 30 ?.?. ???????????? ??????????? ???????? ? ????????? ???????????: ??????? ???????? - ?? 1 ?.?. ?? ??. ??. ???????? ????? - ?? 2 ?.?. ?? ??. ??. ??????? ? ?????????? ?????????? - 120 ?.?. ?? ??.?. ?????????? ?????: ?? 150 ?? ? ????? - 2,27 ?.?. ?? ??. ? ?? 60 ?? ?? 150?? - 4,67 ?.?. ?? ??.?. ?? 4 ?? ?? 60 ?? - 6,79 ?.?. ?? ??.?. ??????? ???????????, ??????. ?????????? ??????? ? ???????? ????. ???????? ???????????! ??????? ?? ?????? ? ??????! ????????????? ??????? ? ???????! ?????????? ? ?????? ?????????, ???????? ? ??????????! ??????????? ????? ?? ????????? ? ???????????? ? ????? ?????????? ?? ?????? ? ?????????! ???? ?????????: ??????, ?????, ???????, ?????????????, ??????, ???????, ????????, ?????????, ?????? ??????, ??????, ?????, ???????-????, ?????????, ????????, ???????, ??????, ?????, ??????, ????????????, ???? ... ?????????: ??????, ??????, ??????, ???????, ??????, ?????, ???, ???????, ??????????, ????????????, ????, ??????, ??????, ???????, ???????, ?????? ... ???? ?????????: ???????????, ???????????, ????????????, ????????????, ???????????, ??????????, ???????? ??????, ??????? ??????, ???????????, ?????????????? ??????, ???????? ??????? ? ???????, ?????????????. ?????????? ? ???????? ?? 1 ???! ???????? ?? ??????????? ????????????!!! ???????????, ???. ??????, ???. ??????, ?????????????, ?????????, ?????????, ?????????????, ????????, ???????, ????????, ???????????, ???, ??? ????? ????????? ??? ??????? ???????! ????? ??????, ???, ? ????????? ???????, ?????, 500 ??. - 265 ?.?. ?????????????, ?/?, 50 ??. - 2,9 ?.?. ?? ????? ???????????? - ???????! ??????????? ????? ?? ???????? ? ??????????? ?? ?????????? ????????? ?????????? ????????? ? ????? ?????????? ?? ?????? ? ?????????! 3. ??????????! ????? ? ?????. ?? 100 ??????? ??????? ?? ???????? ?0. ????????? ?? 6 ??????. ????? ???????? ? ????????????? ?????????. ????????? ?????????, 7?10 ??, ?????. ?????, ??????? 32 ???., 4 + 2 1000 ??. - 140 ?.?., 3000 ??. - 235 ?.?., 5000 ??. - 270 ?.?., 10000 ??. - 390 ?.?. ??????????? ?????????, ??????? ???? 4+0, 1 ???????, 500 ??. - 2,85 ?.?., 3 ???????, 500 ??. - 4,1 ?.?. ????????, ????? ??????, 300 ??./??. ?, ???, 4+2, 500 ??. - 425 ?.?., 1000 ??. - 556 ?.?. ????????, ??????, 2+0, 1000 ??. - 86 ?.?., 3000 ??. - 124 ?.?., 5000 ??. - 172 ?.?. ???????, ?????? ???, 280 ??./?2, ?????, 1+0, 100 ??. - 16,5 ?.?. (???????? ??????? ?? 100 ??.) ???????, August Koehler, 246 ??./?2, ?????, 1+0, 100 ??. - 17,25 ?.?. (???????? ??????? ?? 100 ??.) ???????, ?????? ???, 280 ??./?2, 1+0, 500 ??. - 40,5 ?.?. ???????, August Koehler, 246 ??./?2, 1+0, 500 ??. - 44,25 ?.?. ??????????? ????? ?? ???????, ????????????? ??????? ???????? ? ?????????????! ??????, ?4, 130 ??./?2, 4+4, 2 ?., 1000 ??. - 220 ?.?. ????????? ?????????, 7?10 ??, 4+2, ??????? 32 ???., ??????, 1000 ??. - 120 ?.?. ????????, 20?13 ??, 4+0, 1000 ??. - 0,21 ?.?. ???????, 90?90?90 ??, ????????? 3 ??????? 4+0, ?? ?????? ????? 1+0, 200 ??. - 7,65 ?.?. ???????? ????? ?? ??????, 10?12?2 ??, 2+0, 500 ??. - 2,88 ?.?. ???????????? ?????????????, ??????????, ????????????, ???????? ?????? ?? ??????????? ????????????! ?????????????, ??????, ?????, ??????, ??? ??????? ? ????????, 50 ??. - 135 ?.?. ???????? ??????????????? ?????????: ????????? ??????, ????????, ???????????, ???????, ?????????????, ?????, ??????????, ??????????, ????????, ?????????, ???????? ???????????? ??????????????? ????????? ?? 2 ????! ???????? - ??????! ???????????? ????????, ??????, ???????????? ??????? ?????????????! ??????????? ????? ?? ?????? ?? ??????????????? ????????? ? ????? ?????????? ?? ?????? ? ?????????! 4. ?????????? ??????? ?? ???????????? ?????! 5. ???????. ?????? ????????. ??????? ?????????! ??????, 4+0, 360 d.p.i., ? ????????? ??? ?????????, - 23,5 ?.?./1 ??. ?. ?????????? ??????? ?? ?????. ?????????? ??????? ?? ??????????. ?????????? ??????? ?? ???? - ????????. ?????????? ??????? ?? ????????? ?????????? (???????, ??????????, ???????, ?????????? ?????). ?????????? ??????? ? ????? (?? ???????? ? ? ??????? ???????). 6. ??????. ????? ???????. ????? ?????? ? ?????????????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 7. ?????. ??? ???????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 8. ??. ?????????? ?? GRP ? ?????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 9. ??????? ? ???????????. ???????? ???????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 10. ??????? ? ????????. ???????????? ????????. ??????????? ??????? ? ?????: RU, COM, SU, NET, BIZ, INFO, ORG! ???????? Web-??????? ? ???????????????? ? ????????! ? ??????? ? ????? ??????????? ? ????? ?????????? ?? ?????? ? ?????????! 11. ??????????? ? ?????????? ????? ????????????? ??????????? ? ??????????! ?????????, ?????????-?????, ???????????, ????????????? ???????, ????? ?? ????? ????? ????????? ? ?????! ????????? ?????????! ??????????? ? ????????? ? ?????????? ?? ?????? ? ?????????! 12. ????? ????????? ??? ??????? ? ?????????? ? ?????????! 13. ???????? ? ???????? ???? - ?????????! 14. ????????. ??? ?????? ????????????? ????????, ?? ??? ???? ????????! ????? ?????????? ? ?????? ??????????? ? ??? ?????????. 15. ?????. ?? 12 ????????? - ????????? ???? ?? ?????? ? ?????? ? ?.-??????????! 16. ???? ??????????? ?? ???????????! ???? ???????????????? ????!!! ????????? ?????????? ????????????? ??????!!! ????????? ??? ????? ??????! ???.: (095) 101-3527 ??????????, ?? ????????? ????? ?? ???????? ?????! ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????.