From David.Bauer at SCHERING.DE Thu Dec 1 02:20:12 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 1 Dec 2005 08:20:12 +0100 Subject: [EMBOSS] libpng problems on Solaris 8, png.h version versus png.c version In-Reply-To: Message-ID: Hi David, a had similar trouble with this on Solaris. The best way to get a clean rebuild is to rerun the configure. Watch for the folowing lines in the configure output: ----------------------------------------------------------------------------- checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... yes PNG libraries found ----------------------------------------------------------------------------- Unless you don't get "PNG libraries found" here, you are in trouble ;-) Most often this is caused by the search path for dynamic libraries. On Solaris you may have somwhere in /opt some older version of libgd. You get than a "no" for "gdImageCreateFromPng". If you don't want (or can't) change the libs in system location you can create the complete set of z,gd,png in an alternative location and use the option "--with-pngdriver=DIR" to point configure to this place. But this has to be the complete installation containing also the .h files and not just the libraries. Hope this helps, David. emboss-bounces at emboss.open-bio.org schrieb am 01/12/2005 01:10:17: > This is making me nuts. > > plplot (re)compiled gdpng to create gdpng.o in ..../plplot/.libs, > yet it seems not to be putting it into the libraries. > specify png as the output graphics type with polydot (for intance) > results in it bailing out with: > > Devices allowed are:- > postscript > ps > hpgl > hp7470 > hp7580 > meta > colourps > cps > xwindows > x11 > tektronics > tekt > tek4107t > tek > none > null > text > data > xterm > Error: Invalid graph value 'png' > Died: polydot terminated: Bad value for '-graph' with -auto defined > > Again, how does one do a CLEAN (completely clean) rebuild? > > Thanks, > > David Mathog > mathog at caltech.edu > Manager, Sequence Analysis Facility, Biology Division, Caltech > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From mathog at mendel.bio.caltech.edu Thu Dec 1 14:12:05 2005 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 01 Dec 2005 11:12:05 -0800 Subject: [EMBOSS] libpng problems on Solaris 8, png.h version versus png.c version Message-ID: > > Hi David, > > a had similar trouble with this on Solaris. > The best way to get a clean rebuild is to rerun the configure. > Watch for the folowing lines in the configure output: > ----------------------------------------------------------------------------- > > checking if png driver is wanted... yes > checking for inflateEnd in -lz... yes > checking for png_destroy_read_struct in -lpng... yes > checking for gdImageCreateFromPng in -lgd... yes > PNG libraries found > ----------------------------------------------------------------------------- > > Unless you don't get "PNG libraries found" here, you are in trouble That helped. Sure enough it was failing the test at -lgd above. I found 3, count them 3, different problems that were causing this: 1. There was an older version of libpng in /usr/local/lib along with the current one. For completely incomprehensible reasons that one was being used. Removed it. Then I tried to clear this problem by updating every related bit of software on the platform (autoconf,m4, automake,libtool,libpng, libgd,etc.). None of that helped. Actually it hurt since the more recent version of gd needed fontconfig but happily installed without it. Finally configure was run with 'set -x' and 'set +x' around the problem code. Then the test .c file was copied out during .configure's run and built with the command line that .configure used. This turned up the following: 2. configure was not adding '-liconv' to the compile line so those symbols were not found. 3. the test for gd was dependent on libfontconfig and it wasn't putting -lfontconfig on the command line. Moreover, I didn't even have this package installed. Installed it with pkg-get (as was libpng, and gd). freetype 2.1.10 was installed from source. Solution for 2,3 was: export LDFLAGS='-liconv -lfontconfig' ./configure It still has some problem building in gui though: "No rule to make traget `FileEditorDisplay.PopupListener.html', needed by `all-am' Stop. Maybe that has something to do with the fairly old Perl distro on this system? (5.6.1) Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From golharam at umdnj.edu Fri Dec 2 15:49:01 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 02 Dec 2005 15:49:01 -0500 Subject: [EMBOSS] Custom Scoring Matrix Message-ID: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> I've created a custom scoring matrix of log-odds probabilities for comparing certain types of sequences. I'm not trying to use stretcher to compare two sequences using my matrix. I'm passing in the matrix as an option to stretcher using -datafile: stretcher -asequence a.fasta -bsequence b.fasta -datafile ./matrix.mat I get an error "EMBOSS An error in ajarr.c at line 1752: Bad integer conversion". My matrix looks something like this: A C G T A 1.1619 -0.9808 -0.7169 -1.2463 C -1.1165 1.54077 -0.8689 -0.8288 G -0.7911 -0.8621 1.5170 -1.1425 T -1.2419 -0.7391 -1.0441 1.0995 I take it from the error, strether requires integers. Is that true, or is the error generic? If it requires integers, then I will need to find a way to normalize this matrix to integers. Has anyone done this before? Ryan From easmith at beatrice.rutgers.edu Fri Dec 2 16:27:47 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Fri, 2 Dec 2005 16:27:47 -0500 Subject: [EMBOSS] Custom Scoring Matrix In-Reply-To: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> References: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> Message-ID: In message <072b01c5f781$d32498c0$5022db82 at GOLHARMOBILE1> (on 2 December 2005 15:49:01 -0500), golharam at umdnj.edu (Ryan Golhar) wrote: >I've created a custom scoring matrix of log-odds probabilities for >comparing certain types of sequences. > >I'm not trying to use stretcher to compare two sequences using my >matrix. I'm passing in the matrix as an option to stretcher using >-datafile: > >stretcher -asequence a.fasta -bsequence b.fasta -datafile ./matrix.mat > >I get an error "EMBOSS An error in ajarr.c at line 1752: Bad integer >conversion". > >My matrix looks something like this: > > A C G T >A 1.1619 -0.9808 -0.7169 -1.2463 >C -1.1165 1.54077 -0.8689 -0.8288 >G -0.7911 -0.8621 1.5170 -1.1425 >T -1.2419 -0.7391 -1.0441 1.0995 > >I take it from the error, strether requires integers. It appears so - it is using the AjPMatrix, not AjPMatrixf, datatype, for instance. >Is that true, or is the error generic? If it requires integers, then I >will need to find a way to normalize this matrix to integers. Has anyone >done this before? Yes. If you're needing all the decimal places, I would suggest simply multiplying by 10000 (and ditto for gap open/extend penalties). That at least seems to work... -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity From pmr at ebi.ac.uk Fri Dec 2 17:02:09 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 02 Dec 2005 22:02:09 +0000 Subject: [EMBOSS] Custom Scoring Matrix In-Reply-To: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> References: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> Message-ID: <4390C461.2050106@ebi.ac.uk> Ryan Golhar wrote: > I take it from the error, strether requires integers. Is that true, or > is the error generic? If it requires integers, then I will need to find > a way to normalize this matrix to integers. Has anyone done this > before? Ah, yes ... it does require integers. Not our code, but we may be able to convert it. Meanwhile, needle will run with a floating point matrix. Hope that helps, Peter From golharam at umdnj.edu Mon Dec 5 17:40:48 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 05 Dec 2005 17:40:48 -0500 Subject: [EMBOSS] Stretcher & custom scoring matrix Message-ID: <07b401c5f9ec$f0a217c0$5022db82@GOLHARMOBILE1> I'm using stretcher with a custom scoring matrix I created. It works for 99% of my sequence. Occassionally, I get the waring: Warning: stretcher CheckScore failed I'm using a gapopen penalty of 160000 and gapextend of 40000. This is because I need to normalize my matrix from floating point to integer. I suspect this has something to do with it. What does this error mean? Ryan From godinn at bgumail.bgu.ac.il Tue Dec 6 08:41:12 2005 From: godinn at bgumail.bgu.ac.il (godinn at bgumail.bgu.ac.il) Date: Tue, 6 Dec 2005 15:41:12 +0200 Subject: [EMBOSS] FuzzPro Message-ID: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> Hello. I would like to run a multiple sequence file in FASTA format in the FuzzPro application. How can I do this? I'm working through the BGU GUI. Thanks in advance, Noa Godin. From pmr at ebi.ac.uk Tue Dec 6 09:24:55 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 06 Dec 2005 14:24:55 +0000 Subject: [EMBOSS] FuzzPro In-Reply-To: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> References: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> Message-ID: <43959F37.7030904@ebi.ac.uk> Hi Noa, godinn at bgumail.bgu.ac.il wrote: > Hello. > I would like to run a multiple sequence file in FASTA format in the FuzzPro application. > How can I do this? > I'm working through the BGU GUI. Fuzzpro is designed to read a multiple sequence file. You should be able to give this input file to the BGU server. The results will show the hits in each sequence in the file (look for the sequence name in each subheader). regards, Peter Rice From golharam at umdnj.edu Wed Dec 7 10:29:52 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 07 Dec 2005 10:29:52 -0500 Subject: [EMBOSS] cirdna Message-ID: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> Two questions: Is there a program in EMBOSS to generate an input file for cirdna? Is there a program in EMBOSS to draw a circular piece of DNA and all the restriction sites on that piece of DNA? GCG has a tool to do this, and the closest I see in EMBOSS is cirdna. With GCG, you were able to just supply the DNA sequence and it would do the rest. That doesn't seem to be the case here, or am I missing something? Ryan -- Ryan Golhar - golharam at umdnj.edu The Informatics Institute of UMDNJ From jison at ebi.ac.uk Thu Dec 8 03:38:17 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 8 Dec 2005 08:38:17 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> References: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> Message-ID: <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> Hi Ryan So far as I'm aware there are no apps to generate a cirdna input file, at least not directly. cirdna has a generic concept of the markers which it displays: a marker is typically a gene but could be any genetic feature with a defined range in the sequence. So it depends on what you want to show. If you want to display restriction sites,you could use e.g. restrict or restover to identify the sites, then convert the appropriate parts of the output into a format suitable for cirdna. You'd need to check the input and output formats from the documentation closely: http://emboss.sourceforge.net/apps/cirdna.html http://emboss.sourceforge.net/apps/restrict.html I don't think there are tools in EMBOSS to do that conversion for you at the moment. restrict can generate output as a report format but cirdna can't currently read a report format. That could change though. If you let us know exactly what you need we can do something for a future release. Cheers Jon > Two questions: > > Is there a program in EMBOSS to generate an input file for cirdna? > > Is there a program in EMBOSS to draw a circular piece of DNA and all the > restriction sites on that piece of DNA? GCG has a tool to do this, and > the closest I see in EMBOSS is cirdna. With GCG, you were able to just > supply the DNA sequence and it would do the rest. That doesn't seem to > be the case here, or am I missing something? > > Ryan > > -- > Ryan Golhar - golharam at umdnj.edu > The Informatics Institute of UMDNJ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From pmr at ebi.ac.uk Thu Dec 8 04:27:33 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 8 Dec 2005 09:27:33 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> References: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> Message-ID: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> JOn Ison wrote: > So far as I'm aware there are no apps to generate a cirdna input > file, at least not directly. > > I don't think there are tools in EMBOSS to do that conversion for > you at the moment. restrict can generate output as a report format > but cirdna can't currently read a report format. That could change > though. If you let us know exactly what you need we can do something > for a future release. A word of caution ... I tried exactly this for cirdna and lindna a few years ago (writing their input format as a new report format). Unfortunately, the font sizes and layout in cirdna and lindna did not work in many cases - for large or small sequences there was no good standard input format that produced readable output. Every case needed to be edited. So, we have to also make major changes to cirdna and lindna to support this. Still, if there is enough demands from our users we can do it .... regards, Peter From golharam at umdnj.edu Thu Dec 8 10:30:25 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 08 Dec 2005 10:30:25 -0500 Subject: [EMBOSS] cirdna In-Reply-To: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> Message-ID: <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> We met with a group of our users and and there are quite a few who use MapPlot from GCG to draw plasmids with restriction sites. Migrating from GCG to EMBOSS means we have to provide them with alternatives to whatever tools they used in GCG. Someone else recommended TACG (http://tacg.sourceforge.net/). We'd like our users to use the web front-end (EMBOSS-Explorer by Luke McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to be used by EMBOSS-Explorer. If modifying cirdna is not possible, what about incorporating TACG as a MYEMBOSS application? Ryan -----Original Message----- From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] Sent: Thursday, December 08, 2005 4:28 AM To: emboss at emboss.open-bio.org Cc: golharam at umdnj.edu Subject: Re: [EMBOSS] cirdna JOn Ison wrote: > So far as I'm aware there are no apps to generate a cirdna input file, > at least not directly. > > I don't think there are tools in EMBOSS to do that conversion for you > at the moment. restrict can generate output as a report format > but cirdna can't currently read a report format. That could change > though. If you let us know exactly what you need we can do something > for a future release. A word of caution ... I tried exactly this for cirdna and lindna a few years ago (writing their input format as a new report format). Unfortunately, the font sizes and layout in cirdna and lindna did not work in many cases - for large or small sequences there was no good standard input format that produced readable output. Every case needed to be edited. So, we have to also make major changes to cirdna and lindna to support this. Still, if there is enough demands from our users we can do it .... regards, Peter From jison at ebi.ac.uk Fri Dec 9 13:15:15 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 9 Dec 2005 18:15:15 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> References: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> Message-ID: <41397.172.31.70.94.1134152115.squirrel@webmail.ebi.ac.uk> Hi Ryan The request is now logged which means that we'll certainly take a look at doing something for the next release. If your users have specific requirements or specification for such a program, if you forward them, they could be incorporated into any eventual design. Cheers Jon > We met with a group of our users and and there are quite a few who use > MapPlot from GCG to draw plasmids with restriction sites. Migrating > from GCG to EMBOSS means we have to provide them with alternatives to > whatever tools they used in GCG. > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd like > our users to use the web front-end (EMBOSS-Explorer by Luke McCarthy), > which means any tools must be part of EMBOSS or MYEMBOSS to be used by > EMBOSS-Explorer. If modifying cirdna is not possible, what about > incorporating TACG as a MYEMBOSS application? > > Ryan > > -----Original Message----- > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > Sent: Thursday, December 08, 2005 4:28 AM > To: emboss at emboss.open-bio.org > Cc: golharam at umdnj.edu > Subject: Re: [EMBOSS] cirdna > > > JOn Ison wrote: > >> So far as I'm aware there are no apps to generate a cirdna input file, > >> at least not directly. >> >> I don't think there are tools in EMBOSS to do that conversion for you >> at the moment. restrict can generate output as a report format >> but cirdna can't currently read a report format. That could change >> though. If you let us know exactly what you need we can do something >> for a future release. > > A word of caution ... I tried exactly this for cirdna and lindna a few > years ago (writing their input format as a new report format). > > Unfortunately, the font sizes and layout in cirdna and lindna did not > work in many cases - for large or small sequences there was no good > standard input format that produced readable output. Every case needed > to be edited. > > So, we have to also make major changes to cirdna and lindna to support > this. > > Still, if there is enough demands from our users we can do it .... > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From golharam at umdnj.edu Fri Dec 9 13:24:24 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 09 Dec 2005 13:24:24 -0500 Subject: [EMBOSS] cirdna In-Reply-To: <41397.172.31.70.94.1134152115.squirrel@webmail.ebi.ac.uk> Message-ID: <08c801c5fced$c93b69d0$5022db82@GOLHARMOBILE1> Hi Jon, Thanks. Sure, I'll keep you informed. Right now, I'm only aware of users wanting to be able to map restriction sites in a circular piece of DNA by just inputting their DNA sequence and getting the output from cirdna. If I get anything more specific, I'll let you know. Ryan -----Original Message----- From: Jon Ison [mailto:jison at ebi.ac.uk] Sent: Friday, December 09, 2005 1:15 PM To: golharam at umdnj.edu Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] cirdna Hi Ryan The request is now logged which means that we'll certainly take a look at doing something for the next release. If your users have specific requirements or specification for such a program, if you forward them, they could be incorporated into any eventual design. Cheers Jon > We met with a group of our users and and there are quite a few who use > MapPlot from GCG to draw plasmids with restriction sites. Migrating > from GCG to EMBOSS means we have to provide them with alternatives to > whatever tools they used in GCG. > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd > like our users to use the web front-end (EMBOSS-Explorer by Luke > McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to > be used by EMBOSS-Explorer. If modifying cirdna is not possible, what > about incorporating TACG as a MYEMBOSS application? > > Ryan > > -----Original Message----- > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > Sent: Thursday, December 08, 2005 4:28 AM > To: emboss at emboss.open-bio.org > Cc: golharam at umdnj.edu > Subject: Re: [EMBOSS] cirdna > > > JOn Ison wrote: > >> So far as I'm aware there are no apps to generate a cirdna input >> file, > >> at least not directly. >> >> I don't think there are tools in EMBOSS to do that conversion for you >> at the moment. restrict can generate output as a report format >> but cirdna can't currently read a report format. That could change >> though. If you let us know exactly what you need we can do something >> for a future release. > > A word of caution ... I tried exactly this for cirdna and lindna a few > years ago (writing their input format as a new report format). > > Unfortunately, the font sizes and layout in cirdna and lindna did not > work in many cases - for large or small sequences there was no good > standard input format that produced readable output. Every case needed > to be edited. > > So, we have to also make major changes to cirdna and lindna to support > this. > > Still, if there is enough demands from our users we can do it .... > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From David.Bauer at SCHERING.DE Mon Dec 12 04:54:12 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 12 Dec 2005 10:54:12 +0100 Subject: [EMBOSS] cirdna In-Reply-To: <08c801c5fced$c93b69d0$5022db82@GOLHARMOBILE1> Message-ID: What about replacing cirdna with tacg ? http://tacg.sourceforge.net/ Cheers, David. emboss-bounces at emboss.open-bio.org schrieb am 09/12/2005 19:24:24: > Hi Jon, > > Thanks. Sure, I'll keep you informed. Right now, I'm only aware of > users wanting to be able to map restriction sites in a circular piece of > DNA by just inputting their DNA sequence and getting the output from > cirdna. If I get anything more specific, I'll let you know. > > Ryan > > > -----Original Message----- > From: Jon Ison [mailto:jison at ebi.ac.uk] > Sent: Friday, December 09, 2005 1:15 PM > To: golharam at umdnj.edu > Cc: emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] cirdna > > > Hi Ryan > > The request is now logged which means that we'll certainly take a look > at doing something for the next release. If your users have specific > requirements or specification for such a program, if you forward them, > they could be incorporated into any eventual design. > > Cheers > > Jon > > > > > We met with a group of our users and and there are quite a few who use > > > MapPlot from GCG to draw plasmids with restriction sites. Migrating > > from GCG to EMBOSS means we have to provide them with alternatives to > > whatever tools they used in GCG. > > > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd > > like our users to use the web front-end (EMBOSS-Explorer by Luke > > McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to > > > be used by EMBOSS-Explorer. If modifying cirdna is not possible, what > > > about incorporating TACG as a MYEMBOSS application? > > > > Ryan > > > > -----Original Message----- > > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > > Sent: Thursday, December 08, 2005 4:28 AM > > To: emboss at emboss.open-bio.org > > Cc: golharam at umdnj.edu > > Subject: Re: [EMBOSS] cirdna > > > > > > JOn Ison wrote: > > > >> So far as I'm aware there are no apps to generate a cirdna input > >> file, > > > >> at least not directly. > >> > >> I don't think there are tools in EMBOSS to do that conversion for you > > >> at the moment. restrict can generate output as a report format > >> but cirdna can't currently read a report format. That could change > >> though. If you let us know exactly what you need we can do something > > >> for a future release. > > > > A word of caution ... I tried exactly this for cirdna and lindna a few > > > years ago (writing their input format as a new report format). > > > > Unfortunately, the font sizes and layout in cirdna and lindna did not > > work in many cases - for large or small sequences there was no good > > standard input format that produced readable output. Every case needed > > > to be edited. > > > > So, we have to also make major changes to cirdna and lindna to support > > > this. > > > > Still, if there is enough demands from our users we can do it .... > > > > regards, > > > > Peter > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From indapa at gmail.com Mon Dec 12 16:16:56 2005 From: indapa at gmail.com (Amit Indap) Date: Mon, 12 Dec 2005 16:16:56 -0500 Subject: [EMBOSS] pasteseq Message-ID: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Hi, I'm an EMBOSS newbie but have a simple question. For the pasteseq program I'm trying to paste in the character '-' into my sequence: > pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa But my sequence is unchanged after I run the above command. However if I change insert.fa to be the sequence NN it works fine. Is there anyway I can insert the '-' character Much thanks, Amit Indap Cornell University -- Amit Indap http://www.bscb.cornell.edu/Homepages/Amit_Indap/ From pmr at ebi.ac.uk Tue Dec 13 03:46:00 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 13 Dec 2005 08:46:00 -0000 (GMT) Subject: [EMBOSS] pasteseq In-Reply-To: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Message-ID: <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> Dear Amit, > I'm an EMBOSS newbie but have a simple question. For the pasteseq > program I'm trying to paste in the character '-' into my sequence: > >> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa > > But my sequence is unchanged after I run the above command. However if > I change insert.fa to be the sequence NN it works fine. Is there > anyway I can insert the '-' character Ah ... it seems we have no program that does this easily. pasteseq is really for merging two sequences, rather than sequence editing. However, the reason pasteseq rejects your gaps is because both inputs are of type sequence and have no gaps. It makes sense to allow them. Change emboss/acd/pasteseq.acd to have the sequence input definitions below (only the types have changed) and "make install" again - or, simply copy the pasteseq.acd file to overwrite the installed one in (by default) /usr/local/share/EMBOSS/acd/pasteseq.acd We will make this change in the next release. Hope that helps, Peter ========================== section: input [ information: "Input section" type: "page" ] sequence: asequence [ parameter: "Y" type: "gapany" ] sequence: bsequence [ parameter: "Y" information: "Sequence to insert" type: "@($(acdprotein) ? gapstopprotein : gapnucleotide)" ] endsection: input From ajb at ebi.ac.uk Tue Dec 13 04:29:17 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 13 Dec 2005 09:29:17 -0000 (GMT) Subject: [EMBOSS] pasteseq In-Reply-To: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Message-ID: <50580.81.96.70.96.1134466157.squirrel@webmail.ebi.ac.uk> Alternatively you might be able to use 'biosed'. That program will replace all occurrences of a sequence string with a replacement string. As it replaces all occurrences you need to be careful about uniqueness. So, if your sequence file (myseq.seq) was: >MYSEQ ACDEFGHI You could use the following to insert a gap at the start: biosed -target "ACDE" -replace "-ACDE" myseq.seq Alan > Hi, > > I'm an EMBOSS newbie but have a simple question. For the pasteseq > program I'm trying to paste in the character '-' into my sequence: > >> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa > > But my sequence is unchanged after I run the above command. However if > I change insert.fa to be the sequence NN it works fine. Is there > anyway I can insert the '-' character > > Much thanks, > > Amit Indap > Cornell University > > > > > > -- > Amit Indap > http://www.bscb.cornell.edu/Homepages/Amit_Indap/ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Tue Dec 13 04:53:00 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 13 Dec 2005 09:53:00 -0000 (GMT) Subject: [EMBOSS] EMBOSS Developers Course Message-ID: <40248.172.31.100.168.1134467580.squirrel@webmail.ebi.ac.uk> Hi Details on a forthcoming programming course for bioinformatics using EMBOSS are below. Apologies for the email if not interested. Please distribute to your colleagues who might be interested in this. Best regards Jon Ison The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK E-mail : jison at ebi.ac.uk BSDC 2006 Bioinformatics Software Development Course January 18-20, April 18-20 2006 Following from the popular BSDC 2003/2004 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 18-20 and April 18-20, 2006. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required to get the most out of the course, familiarity with pointers is helpful but not essential. That said, all are welcome regardless of background or experience. Places are limited and the two dates are likely to get booked up quickly so please email Liz Ford (ford at ebi.ac.uk) to register as soon as possible. We do not make a profit on the course but must charge ?125 / person (for the 3-days) to recover some of our costs. To read more about the course see http://emboss.sourceforge.net/developers/developers_course/ (1) To read more about EMBOSS see http://emboss.sourceforge.net/ To register email Liz Ford (ford at ebi.ac.uk) For further information email Jon Ison (jison at ebi.ac.uk) (1) Please note, the course is currently being revised. The course schedule is correct but details for talks & practicals are subject to change. From indapa at gmail.com Tue Dec 13 10:10:12 2005 From: indapa at gmail.com (Amit Indap) Date: Tue, 13 Dec 2005 10:10:12 -0500 Subject: [EMBOSS] pasteseq In-Reply-To: <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> Message-ID: <3cfaa4040512130710l1d62777bo62dfdfb194e60ff4@mail.gmail.com> Hi Peter, Thanks for the help. I modified the pasteseq.acd file and am now able to put in gap characters. Amit Indap > Ah ... it seems we have no program that does this easily. pasteseq is > really for merging two sequences, rather than sequence editing. > > However, the reason pasteseq rejects your gaps is because both inputs are > of type sequence and have no gaps. > > It makes sense to allow them. Change emboss/acd/pasteseq.acd to have the > sequence input definitions below (only the types have changed) and "make > install" again - or, simply copy the pasteseq.acd file to overwrite the > installed one in (by default) /usr/local/share/EMBOSS/acd/pasteseq.acd > > We will make this change in the next release. > > Hope that helps, > > Peter > > ========================== > > section: input [ > information: "Input section" > type: "page" > ] > > sequence: asequence [ > parameter: "Y" > type: "gapany" > ] > > sequence: bsequence [ > parameter: "Y" > information: "Sequence to insert" > type: "@($(acdprotein) ? gapstopprotein : gapnucleotide)" > ] > > endsection: input > > > > > -- Amit Indap http://www.bscb.cornell.edu/Homepages/Amit_Indap/ From Kevin.M.Brown at asu.edu Wed Dec 14 11:18:17 2005 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 14 Dec 2005 09:18:17 -0700 Subject: [EMBOSS] CAI Tables Message-ID: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> I've searched the archives and the Net trying to find more information the list of highly-expressed genes that CAI used to create the codon tables for the various species. Does anyone know where these tables came from? From imj15 at student.canterbury.ac.nz Wed Dec 14 18:41:01 2005 From: imj15 at student.canterbury.ac.nz (Iris Vargas Jentzsch) Date: Thu, 15 Dec 2005 12:41:01 +1300 Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 Message-ID: <43A0AD8D.4050909@student.canterbury.ac.nz> Hello everybody, I need some help here. My recent tries to install EMBOSS-3.0.0 have been mostly unsuccessfull. I am working with a Fedora Core 4 Linux installation. After ./configure when I issue the command make, at the beginning it seems to work fine but it gets to some point in /pkg/EMBOSS-3.0.0/emboss/data after installing the libraries I guess, where it can?t go further. Here are the messages I get, I did cut a huge part in the middle that seemed to have no error messages (although it seemed to be the same over and over again... however if someone needs the whole long message I can post it. [root at localhost EMBOSS-3.0.0]# make Making all in plplot make[1]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' Making all in lib make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot/lib' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/plplot/lib' make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" -DEMBOSS_TOP=\"/pkg/EMBOSS-3.0.0\" -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT pdfutils.lo -MD -MP -MF ".deps/pdfutils.Tpo" -c -o pdfutils.lo pdfutils.c; \ then mv -f ".deps/pdfutils.Tpo" ".deps/pdfutils.Plo"; else rm -f ".deps/pdfutils.Tpo"; exit 1; fi mkdir .libs . . . . . gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF .deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF .deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o libnucleus.la -rpath /usr/local/lib -version-info 3:0:0 embaln.lo embcom.lo embcons.lo embdata.lo embdbi.lo embdmx.lo embdomain.lo embest.lo embexit.lo embgroup.lo embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo embmol.lo embnmer.lo embpat.lo embprop.lo embpdb.lo embread.lo embsig.lo embshow.lo embword.lo gcc -shared .libs/embaln.o .libs/embcom.o .libs/embcons.o .libs/embdata.o .libs/embdbi.o .libs/embdmx.o .libs/embdomain.o .libs/embest.o .libs/embexit.o .libs/embgroup.o .libs/embiep.o .libs/embindex.o .libs/embinit.o .libs/embmat.o .libs/embmisc.o .libs/embmol.o .libs/embnmer.o .libs/embpat.o .libs/embprop.o .libs/embpdb.o .libs/embread.o .libs/embsig.o .libs/embshow.o .libs/embword.o -Wl,-soname -Wl,libnucleus.so.3 -o .libs/libnucleus.so.3.0.0 (cd .libs && rm -f libnucleus.so.3 && ln -s libnucleus.so.3.0.0 libnucleus.so.3) (cd .libs && rm -f libnucleus.so && ln -s libnucleus.so.3.0.0 libnucleus.so) ar cru .libs/libnucleus.a embaln.o embcom.o embcons.o embdata.o embdbi.o embdmx.o embdomain.o embest.o embexit.o embgroup.o embiep.o embindex.o embinit.o embmat.o embmisc.o embmol.o embnmer.o embpat.o embprop.o embpdb.o embread.o embsig.o embshow.o embword.o ranlib .libs/libnucleus.a creating libnucleus.la (cd .libs && rm -f libnucleus.la && ln -s ../libnucleus.la libnucleus.la) make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/nucleus' Making all in emboss make[1]: Entering directory `/pkg/EMBOSS-3.0.0/emboss' Making all in acd make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/acd' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/acd' Making all in data make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' Making all in AAINDEX make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' Making all in CODONS make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' Making all in REBASE make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' Making all in PRINTS make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' Making all in PROSITE make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' make[3]: *** No rule to make target `EBLOSUMN', needed by `all-am'. Stop. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss' make: *** [all-recursive] Error 1 I?ll appreciate very much if you can give me a hand with this. Thank you! Iris From idrummon at receptor.mgh.harvard.edu Thu Dec 15 11:10:26 2005 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Thu, 15 Dec 2005 11:10:26 -0500 Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 In-Reply-To: <43A0AD8D.4050909@student.canterbury.ac.nz> Message-ID: is it possible that you are missing some of the graphics components that are dependencies for installing emboss? does the output of the configure process show any components "not found". one way to find out if this is a problem would be to configure the emboss install without using some of the graphics components. in the configure -help for instance: --with-pngdriver=DIR root directory path of png/gd/zlib installation defaults to /usr --without-pngdriver to disable pngdriver usage completely good luck -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Nephrology Division, Massachusetts General Hospital Mailing address: Nephrology Division / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: Iris Vargas Jentzsch > Date: Thu, 15 Dec 2005 12:41:01 +1300 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 > > Hello everybody, > > I need some help here. My recent tries to install EMBOSS-3.0.0 have been > mostly unsuccessfull. I am working with a Fedora Core 4 Linux > installation. After ./configure when I issue the command make, at the > beginning it seems to work fine but it gets to some point in > /pkg/EMBOSS-3.0.0/emboss/data after installing the libraries I guess, > where it can?t go further. Here are the messages I get, I did cut a huge > part in the middle that seemed to have no error messages (although it > seemed to be the same over and over again... however if someone needs > the whole long message I can post it. > > [root at localhost EMBOSS-3.0.0]# make > Making all in plplot > make[1]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' > Making all in lib > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot/lib' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/plplot/lib' > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' > if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" > -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 > -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 > -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 > -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I/usr/X11R6/include > -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" > -DEMBOSS_TOP=\"/pkg/EMBOSS-3.0.0\" -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 > -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT > pdfutils.lo -MD -MP -MF ".deps/pdfutils.Tpo" -c -o pdfutils.lo pdfutils.c; \ > then mv -f ".deps/pdfutils.Tpo" ".deps/pdfutils.Plo"; else rm -f > ".deps/pdfutils.Tpo"; exit 1; fi > mkdir .libs > . > . > . > . > . > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 > -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 > -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 > -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax > -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF > .deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 > -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 > -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 > -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax > -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF > .deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1 > /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o libnucleus.la -rpath > /usr/local/lib -version-info 3:0:0 embaln.lo embcom.lo embcons.lo > embdata.lo embdbi.lo embdmx.lo embdomain.lo embest.lo embexit.lo > embgroup.lo embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo > embmol.lo embnmer.lo embpat.lo embprop.lo embpdb.lo embread.lo embsig.lo > embshow.lo embword.lo > gcc -shared .libs/embaln.o .libs/embcom.o .libs/embcons.o > .libs/embdata.o .libs/embdbi.o .libs/embdmx.o .libs/embdomain.o > .libs/embest.o .libs/embexit.o .libs/embgroup.o .libs/embiep.o > .libs/embindex.o .libs/embinit.o .libs/embmat.o .libs/embmisc.o > .libs/embmol.o .libs/embnmer.o .libs/embpat.o .libs/embprop.o > .libs/embpdb.o .libs/embread.o .libs/embsig.o .libs/embshow.o > .libs/embword.o -Wl,-soname -Wl,libnucleus.so.3 -o .libs/libnucleus.so.3.0.0 > (cd .libs && rm -f libnucleus.so.3 && ln -s libnucleus.so.3.0.0 > libnucleus.so.3) > (cd .libs && rm -f libnucleus.so && ln -s libnucleus.so.3.0.0 libnucleus.so) > ar cru .libs/libnucleus.a embaln.o embcom.o embcons.o embdata.o embdbi.o > embdmx.o embdomain.o embest.o embexit.o embgroup.o embiep.o embindex.o > embinit.o embmat.o embmisc.o embmol.o embnmer.o embpat.o embprop.o > embpdb.o embread.o embsig.o embshow.o embword.o > ranlib .libs/libnucleus.a > creating libnucleus.la > (cd .libs && rm -f libnucleus.la && ln -s ../libnucleus.la libnucleus.la) > make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/nucleus' > Making all in emboss > make[1]: Entering directory `/pkg/EMBOSS-3.0.0/emboss' > Making all in acd > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/acd' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/acd' > Making all in data > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' > Making all in AAINDEX > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' > Making all in CODONS > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' > Making all in REBASE > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' > Making all in PRINTS > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' > Making all in PROSITE > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[3]: *** No rule to make target `EBLOSUMN', needed by `all-am'. Stop. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss' > make: *** [all-recursive] Error 1 > > > I?ll appreciate very much if you can give me a hand with this. Thank you! > > Iris > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Tue Dec 20 05:18:17 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Dec 2005 10:18:17 +0000 Subject: [EMBOSS] CAI Tables In-Reply-To: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> Message-ID: <43A7DA69.2040405@ebi.ac.uk> Kevin Brown wrote: > I've searched the archives and the Net trying to find more information > the list of highly-expressed genes that CAI used to create the codon > tables for the various species. Does anyone know where these tables > came from? Well, it is a long story ... The original CAI (Codon Adaptation Index) was calculated for S. cerevisiae and used a set of 24 genes (ribosomal proteins, for example) that were known to be highly expressed. Many years ago when I wrote a program to calculate the codon usage for S. pombe (fission yeast) in a program called "codfish", I created a table for the few S. pombe genes from the same set that had already been sequenced. On arriving at the Sanger Centre, where they were sequencing a lot of S. cerevisiae, I needed the codon usage table for the original CAI - and found that when I used the current gene sequences I got the wrong answer. After some tweaking I was able to reconstruct the original versions of the cerevisiae sequences and could reproduce the "standard" CAI values. The differences were minor - mainly missed short 5' exons. The tables Eyeast_cai.cod and Eschpo_cai.cut are the result of these two tables. There are, for historic reasons, copies of these tables with no headers and different names which are "obsolete" and will disappear in EMBOSS 4.0.0. As for "codfish" ... it implemented an algorithm from Frank Wright to calculate the effective number of codons. Frank is a vegan (does not eat codfish), so in EMBOSS we renamed it "chips" :-) Hope that helps! Peter From hegedus at biomembrane.hu Tue Dec 20 08:17:18 2005 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Tue, 20 Dec 2005 08:17:18 -0500 Subject: [EMBOSS] CAI Tables In-Reply-To: <43A7DA69.2040405@ebi.ac.uk> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> <43A7DA69.2040405@ebi.ac.uk> Message-ID: <43A8045E.1050905@biomembrane.hu> Hi, I am not a CAI expert; I also could not find one around me; reading was not enough for me in this topic. So I would like to take the opportunity to ask a CAI (not EMBOSS) related question. What can you tell me about human (mammalian) CAI tables? What do you think/know about the FOP values introduced by Lavner & Kotlar? http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15716084&query_hl=1 I would like to use some measure to predict the translation speed of certain regions in some proteins I am interested in. Thanks, Tamas Peter Rice wrote: > Kevin Brown wrote: > > >>I've searched the archives and the Net trying to find more information >>the list of highly-expressed genes that CAI used to create the codon >>tables for the various species. Does anyone know where these tables >>came from? > > > Well, it is a long story ... > > The original CAI (Codon Adaptation Index) was calculated for S. cerevisiae and > used a set of 24 genes (ribosomal proteins, for example) that were known to be > highly expressed. > > Many years ago when I wrote a program to calculate the codon usage for S. > pombe (fission yeast) in a program called "codfish", I created a table for the > few S. pombe genes from the same set that had already been sequenced. > > On arriving at the Sanger Centre, where they were sequencing a lot of S. > cerevisiae, I needed the codon usage table for the original CAI - and found > that when I used the current gene sequences I got the wrong answer. > > After some tweaking I was able to reconstruct the original versions of the > cerevisiae sequences and could reproduce the "standard" CAI values. The > differences were minor - mainly missed short 5' exons. > > The tables Eyeast_cai.cod and Eschpo_cai.cut are the result of these two > tables. There are, for historic reasons, copies of these tables with no > headers and different names which are "obsolete" and will disappear in EMBOSS > 4.0.0. > > As for "codfish" ... it implemented an algorithm from Frank Wright to > calculate the effective number of codons. Frank is a vegan (does not eat > codfish), so in EMBOSS we renamed it "chips" :-) > > Hope that helps! > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Tue Dec 20 08:59:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Dec 2005 13:59:00 +0000 Subject: [EMBOSS] CAI Tables In-Reply-To: <43A8045E.1050905@biomembrane.hu> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> <43A7DA69.2040405@ebi.ac.uk> <43A8045E.1050905@biomembrane.hu> Message-ID: <43A80E24.20008@ebi.ac.uk> Tamas Hegedus wrote: > Hi, > > I am not a CAI expert; I also could not find one around me; reading was > not enough for me in this topic. > So I would like to take the opportunity to ask a CAI (not EMBOSS) > related question. > > What can you tell me about human (mammalian) CAI tables? > What do you think/know about the FOP values introduced by Lavner & Kotlar? > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15716084&query_hl=1 > > > I would like to use some measure to predict the translation speed of > certain regions in some proteins I am interested in. Well, I am not really a CAI expert either. I hope there is someone better informed who can help. I do like the "unaffected by amino acid composition" part of their statistic, but that may be just my bias. If this statistic would be useful, we can try to implement it in EMBOSS. Any opinions? regards, Peter From golharam at umdnj.edu Wed Dec 21 13:45:48 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 21 Dec 2005 13:45:48 -0500 Subject: [EMBOSS] EDNAFULL Message-ID: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> Does anyone know know how EDNAFULL was derived? Ie, How were the scores it uses determined? Google Scholar didn't turn anything up and I'm not finding anything in the EMBOSS documentation... Ryan From pmr at ebi.ac.uk Thu Dec 22 04:02:34 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 22 Dec 2005 09:02:34 -0000 (GMT) Subject: [EMBOSS] EDNAFULL In-Reply-To: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> References: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> Message-ID: <1376.86.137.131.158.1135242154.squirrel@webmail.ebi.ac.uk> Ryan Golhar writes: > Does anyone know know how EDNAFULL was derived? Ie, How were the scores > it uses determined? > > Google Scholar didn't turn anything up and I'm not finding anything in > the EMBOSS documentation... We should add more information to the header in the matrix file. Will do for the next release. The DNA matrices are simply the ones supplied by NCBI in ftp://ftp.ncbi.nih.gov/blast/matrices/ as files NUC4.2 (EDNAMAT) and NUC4.4 (EDNAFULL). NUC4.2 simply scores 5 for a match, and -4 for a mismatch. NUC4.4 scores 5 for a match, but provides appropriate scores for ambiguity codes so that, for example, R:A scores +1 (rounded up average of -4, -4, 5, 5) The matrices were created by Todd Lowe in 1992. I am not sure where Todd was working at that time. Hope that helps, Peter Rice From ajb at ebi.ac.uk Fri Dec 23 03:45:35 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 23 Dec 2005 08:45:35 -0000 (GMT) Subject: [EMBOSS] Updated dbx* applications Message-ID: <52044.81.96.70.96.1135327535.squirrel@webmail.ebi.ac.uk> These applications have been rewritten to cope with an unlimited number of duplicates (e.g. EMBL WGS file accession numbers). The replacement files are now on our ftp server. ftp://emboss.open-bio.org:/pub/EMBOSS/fixes/ Look at the README file in that directory to see which files you need. Some speed-ups have also been added and the programs now honour the directory settings in emboss.default. Alan From mathog at mendel.bio.caltech.edu Thu Dec 1 00:10:17 2005 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Wed, 30 Nov 2005 16:10:17 -0800 Subject: [EMBOSS] libpng problems on Solaris 8, png.h version versus png.c version Message-ID: This is making me nuts. plplot (re)compiled gdpng to create gdpng.o in ..../plplot/.libs, yet it seems not to be putting it into the libraries. specify png as the output graphics type with polydot (for intance) results in it bailing out with: Devices allowed are:- postscript ps hpgl hp7470 hp7580 meta colourps cps xwindows x11 tektronics tekt tek4107t tek none null text data xterm Error: Invalid graph value 'png' Died: polydot terminated: Bad value for '-graph' with -auto defined Again, how does one do a CLEAN (completely clean) rebuild? Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From David.Bauer at SCHERING.DE Thu Dec 1 07:20:12 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 1 Dec 2005 08:20:12 +0100 Subject: [EMBOSS] libpng problems on Solaris 8, png.h version versus png.c version In-Reply-To: Message-ID: Hi David, a had similar trouble with this on Solaris. The best way to get a clean rebuild is to rerun the configure. Watch for the folowing lines in the configure output: ----------------------------------------------------------------------------- checking if png driver is wanted... yes checking for inflateEnd in -lz... yes checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... yes PNG libraries found ----------------------------------------------------------------------------- Unless you don't get "PNG libraries found" here, you are in trouble ;-) Most often this is caused by the search path for dynamic libraries. On Solaris you may have somwhere in /opt some older version of libgd. You get than a "no" for "gdImageCreateFromPng". If you don't want (or can't) change the libs in system location you can create the complete set of z,gd,png in an alternative location and use the option "--with-pngdriver=DIR" to point configure to this place. But this has to be the complete installation containing also the .h files and not just the libraries. Hope this helps, David. emboss-bounces at emboss.open-bio.org schrieb am 01/12/2005 01:10:17: > This is making me nuts. > > plplot (re)compiled gdpng to create gdpng.o in ..../plplot/.libs, > yet it seems not to be putting it into the libraries. > specify png as the output graphics type with polydot (for intance) > results in it bailing out with: > > Devices allowed are:- > postscript > ps > hpgl > hp7470 > hp7580 > meta > colourps > cps > xwindows > x11 > tektronics > tekt > tek4107t > tek > none > null > text > data > xterm > Error: Invalid graph value 'png' > Died: polydot terminated: Bad value for '-graph' with -auto defined > > Again, how does one do a CLEAN (completely clean) rebuild? > > Thanks, > > David Mathog > mathog at caltech.edu > Manager, Sequence Analysis Facility, Biology Division, Caltech > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From mathog at mendel.bio.caltech.edu Thu Dec 1 19:12:05 2005 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Thu, 01 Dec 2005 11:12:05 -0800 Subject: [EMBOSS] libpng problems on Solaris 8, png.h version versus png.c version Message-ID: > > Hi David, > > a had similar trouble with this on Solaris. > The best way to get a clean rebuild is to rerun the configure. > Watch for the folowing lines in the configure output: > ----------------------------------------------------------------------------- > > checking if png driver is wanted... yes > checking for inflateEnd in -lz... yes > checking for png_destroy_read_struct in -lpng... yes > checking for gdImageCreateFromPng in -lgd... yes > PNG libraries found > ----------------------------------------------------------------------------- > > Unless you don't get "PNG libraries found" here, you are in trouble That helped. Sure enough it was failing the test at -lgd above. I found 3, count them 3, different problems that were causing this: 1. There was an older version of libpng in /usr/local/lib along with the current one. For completely incomprehensible reasons that one was being used. Removed it. Then I tried to clear this problem by updating every related bit of software on the platform (autoconf,m4, automake,libtool,libpng, libgd,etc.). None of that helped. Actually it hurt since the more recent version of gd needed fontconfig but happily installed without it. Finally configure was run with 'set -x' and 'set +x' around the problem code. Then the test .c file was copied out during .configure's run and built with the command line that .configure used. This turned up the following: 2. configure was not adding '-liconv' to the compile line so those symbols were not found. 3. the test for gd was dependent on libfontconfig and it wasn't putting -lfontconfig on the command line. Moreover, I didn't even have this package installed. Installed it with pkg-get (as was libpng, and gd). freetype 2.1.10 was installed from source. Solution for 2,3 was: export LDFLAGS='-liconv -lfontconfig' ./configure It still has some problem building in gui though: "No rule to make traget `FileEditorDisplay.PopupListener.html', needed by `all-am' Stop. Maybe that has something to do with the fairly old Perl distro on this system? (5.6.1) Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From golharam at umdnj.edu Fri Dec 2 20:49:01 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 02 Dec 2005 15:49:01 -0500 Subject: [EMBOSS] Custom Scoring Matrix Message-ID: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> I've created a custom scoring matrix of log-odds probabilities for comparing certain types of sequences. I'm not trying to use stretcher to compare two sequences using my matrix. I'm passing in the matrix as an option to stretcher using -datafile: stretcher -asequence a.fasta -bsequence b.fasta -datafile ./matrix.mat I get an error "EMBOSS An error in ajarr.c at line 1752: Bad integer conversion". My matrix looks something like this: A C G T A 1.1619 -0.9808 -0.7169 -1.2463 C -1.1165 1.54077 -0.8689 -0.8288 G -0.7911 -0.8621 1.5170 -1.1425 T -1.2419 -0.7391 -1.0441 1.0995 I take it from the error, strether requires integers. Is that true, or is the error generic? If it requires integers, then I will need to find a way to normalize this matrix to integers. Has anyone done this before? Ryan From easmith at beatrice.rutgers.edu Fri Dec 2 21:27:47 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Fri, 2 Dec 2005 16:27:47 -0500 Subject: [EMBOSS] Custom Scoring Matrix In-Reply-To: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> References: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> Message-ID: In message <072b01c5f781$d32498c0$5022db82 at GOLHARMOBILE1> (on 2 December 2005 15:49:01 -0500), golharam at umdnj.edu (Ryan Golhar) wrote: >I've created a custom scoring matrix of log-odds probabilities for >comparing certain types of sequences. > >I'm not trying to use stretcher to compare two sequences using my >matrix. I'm passing in the matrix as an option to stretcher using >-datafile: > >stretcher -asequence a.fasta -bsequence b.fasta -datafile ./matrix.mat > >I get an error "EMBOSS An error in ajarr.c at line 1752: Bad integer >conversion". > >My matrix looks something like this: > > A C G T >A 1.1619 -0.9808 -0.7169 -1.2463 >C -1.1165 1.54077 -0.8689 -0.8288 >G -0.7911 -0.8621 1.5170 -1.1425 >T -1.2419 -0.7391 -1.0441 1.0995 > >I take it from the error, strether requires integers. It appears so - it is using the AjPMatrix, not AjPMatrixf, datatype, for instance. >Is that true, or is the error generic? If it requires integers, then I >will need to find a way to normalize this matrix to integers. Has anyone >done this before? Yes. If you're needing all the decimal places, I would suggest simply multiplying by 10000 (and ditto for gap open/extend penalties). That at least seems to work... -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity From pmr at ebi.ac.uk Fri Dec 2 22:02:09 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 02 Dec 2005 22:02:09 +0000 Subject: [EMBOSS] Custom Scoring Matrix In-Reply-To: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> References: <072b01c5f781$d32498c0$5022db82@GOLHARMOBILE1> Message-ID: <4390C461.2050106@ebi.ac.uk> Ryan Golhar wrote: > I take it from the error, strether requires integers. Is that true, or > is the error generic? If it requires integers, then I will need to find > a way to normalize this matrix to integers. Has anyone done this > before? Ah, yes ... it does require integers. Not our code, but we may be able to convert it. Meanwhile, needle will run with a floating point matrix. Hope that helps, Peter From golharam at umdnj.edu Mon Dec 5 22:40:48 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 05 Dec 2005 17:40:48 -0500 Subject: [EMBOSS] Stretcher & custom scoring matrix Message-ID: <07b401c5f9ec$f0a217c0$5022db82@GOLHARMOBILE1> I'm using stretcher with a custom scoring matrix I created. It works for 99% of my sequence. Occassionally, I get the waring: Warning: stretcher CheckScore failed I'm using a gapopen penalty of 160000 and gapextend of 40000. This is because I need to normalize my matrix from floating point to integer. I suspect this has something to do with it. What does this error mean? Ryan From godinn at bgumail.bgu.ac.il Tue Dec 6 13:41:12 2005 From: godinn at bgumail.bgu.ac.il (godinn at bgumail.bgu.ac.il) Date: Tue, 6 Dec 2005 15:41:12 +0200 Subject: [EMBOSS] FuzzPro Message-ID: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> Hello. I would like to run a multiple sequence file in FASTA format in the FuzzPro application. How can I do this? I'm working through the BGU GUI. Thanks in advance, Noa Godin. From pmr at ebi.ac.uk Tue Dec 6 14:24:55 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 06 Dec 2005 14:24:55 +0000 Subject: [EMBOSS] FuzzPro In-Reply-To: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> References: <20051206133518.8D9AA33E62@smtp2.bgu.ac.il> Message-ID: <43959F37.7030904@ebi.ac.uk> Hi Noa, godinn at bgumail.bgu.ac.il wrote: > Hello. > I would like to run a multiple sequence file in FASTA format in the FuzzPro application. > How can I do this? > I'm working through the BGU GUI. Fuzzpro is designed to read a multiple sequence file. You should be able to give this input file to the BGU server. The results will show the hits in each sequence in the file (look for the sequence name in each subheader). regards, Peter Rice From golharam at umdnj.edu Wed Dec 7 15:29:52 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 07 Dec 2005 10:29:52 -0500 Subject: [EMBOSS] cirdna Message-ID: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> Two questions: Is there a program in EMBOSS to generate an input file for cirdna? Is there a program in EMBOSS to draw a circular piece of DNA and all the restriction sites on that piece of DNA? GCG has a tool to do this, and the closest I see in EMBOSS is cirdna. With GCG, you were able to just supply the DNA sequence and it would do the rest. That doesn't seem to be the case here, or am I missing something? Ryan -- Ryan Golhar - golharam at umdnj.edu The Informatics Institute of UMDNJ From jison at ebi.ac.uk Thu Dec 8 08:38:17 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 8 Dec 2005 08:38:17 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> References: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> Message-ID: <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> Hi Ryan So far as I'm aware there are no apps to generate a cirdna input file, at least not directly. cirdna has a generic concept of the markers which it displays: a marker is typically a gene but could be any genetic feature with a defined range in the sequence. So it depends on what you want to show. If you want to display restriction sites,you could use e.g. restrict or restover to identify the sites, then convert the appropriate parts of the output into a format suitable for cirdna. You'd need to check the input and output formats from the documentation closely: http://emboss.sourceforge.net/apps/cirdna.html http://emboss.sourceforge.net/apps/restrict.html I don't think there are tools in EMBOSS to do that conversion for you at the moment. restrict can generate output as a report format but cirdna can't currently read a report format. That could change though. If you let us know exactly what you need we can do something for a future release. Cheers Jon > Two questions: > > Is there a program in EMBOSS to generate an input file for cirdna? > > Is there a program in EMBOSS to draw a circular piece of DNA and all the > restriction sites on that piece of DNA? GCG has a tool to do this, and > the closest I see in EMBOSS is cirdna. With GCG, you were able to just > supply the DNA sequence and it would do the rest. That doesn't seem to > be the case here, or am I missing something? > > Ryan > > -- > Ryan Golhar - golharam at umdnj.edu > The Informatics Institute of UMDNJ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From pmr at ebi.ac.uk Thu Dec 8 09:27:33 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 8 Dec 2005 09:27:33 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> References: <084c01c5fb43$119f2470$5022db82@GOLHARMOBILE1> <44236.172.31.70.94.1134031097.squirrel@webmail.ebi.ac.uk> Message-ID: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> JOn Ison wrote: > So far as I'm aware there are no apps to generate a cirdna input > file, at least not directly. > > I don't think there are tools in EMBOSS to do that conversion for > you at the moment. restrict can generate output as a report format > but cirdna can't currently read a report format. That could change > though. If you let us know exactly what you need we can do something > for a future release. A word of caution ... I tried exactly this for cirdna and lindna a few years ago (writing their input format as a new report format). Unfortunately, the font sizes and layout in cirdna and lindna did not work in many cases - for large or small sequences there was no good standard input format that produced readable output. Every case needed to be edited. So, we have to also make major changes to cirdna and lindna to support this. Still, if there is enough demands from our users we can do it .... regards, Peter From golharam at umdnj.edu Thu Dec 8 15:30:25 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 08 Dec 2005 10:30:25 -0500 Subject: [EMBOSS] cirdna In-Reply-To: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> Message-ID: <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> We met with a group of our users and and there are quite a few who use MapPlot from GCG to draw plasmids with restriction sites. Migrating from GCG to EMBOSS means we have to provide them with alternatives to whatever tools they used in GCG. Someone else recommended TACG (http://tacg.sourceforge.net/). We'd like our users to use the web front-end (EMBOSS-Explorer by Luke McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to be used by EMBOSS-Explorer. If modifying cirdna is not possible, what about incorporating TACG as a MYEMBOSS application? Ryan -----Original Message----- From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] Sent: Thursday, December 08, 2005 4:28 AM To: emboss at emboss.open-bio.org Cc: golharam at umdnj.edu Subject: Re: [EMBOSS] cirdna JOn Ison wrote: > So far as I'm aware there are no apps to generate a cirdna input file, > at least not directly. > > I don't think there are tools in EMBOSS to do that conversion for you > at the moment. restrict can generate output as a report format > but cirdna can't currently read a report format. That could change > though. If you let us know exactly what you need we can do something > for a future release. A word of caution ... I tried exactly this for cirdna and lindna a few years ago (writing their input format as a new report format). Unfortunately, the font sizes and layout in cirdna and lindna did not work in many cases - for large or small sequences there was no good standard input format that produced readable output. Every case needed to be edited. So, we have to also make major changes to cirdna and lindna to support this. Still, if there is enough demands from our users we can do it .... regards, Peter From jison at ebi.ac.uk Fri Dec 9 18:15:15 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 9 Dec 2005 18:15:15 -0000 (GMT) Subject: [EMBOSS] cirdna In-Reply-To: <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> References: <3883.86.137.131.158.1134034053.squirrel@webmail.ebi.ac.uk> <087f01c5fc0c$5038bd30$5022db82@GOLHARMOBILE1> Message-ID: <41397.172.31.70.94.1134152115.squirrel@webmail.ebi.ac.uk> Hi Ryan The request is now logged which means that we'll certainly take a look at doing something for the next release. If your users have specific requirements or specification for such a program, if you forward them, they could be incorporated into any eventual design. Cheers Jon > We met with a group of our users and and there are quite a few who use > MapPlot from GCG to draw plasmids with restriction sites. Migrating > from GCG to EMBOSS means we have to provide them with alternatives to > whatever tools they used in GCG. > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd like > our users to use the web front-end (EMBOSS-Explorer by Luke McCarthy), > which means any tools must be part of EMBOSS or MYEMBOSS to be used by > EMBOSS-Explorer. If modifying cirdna is not possible, what about > incorporating TACG as a MYEMBOSS application? > > Ryan > > -----Original Message----- > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > Sent: Thursday, December 08, 2005 4:28 AM > To: emboss at emboss.open-bio.org > Cc: golharam at umdnj.edu > Subject: Re: [EMBOSS] cirdna > > > JOn Ison wrote: > >> So far as I'm aware there are no apps to generate a cirdna input file, > >> at least not directly. >> >> I don't think there are tools in EMBOSS to do that conversion for you >> at the moment. restrict can generate output as a report format >> but cirdna can't currently read a report format. That could change >> though. If you let us know exactly what you need we can do something >> for a future release. > > A word of caution ... I tried exactly this for cirdna and lindna a few > years ago (writing their input format as a new report format). > > Unfortunately, the font sizes and layout in cirdna and lindna did not > work in many cases - for large or small sequences there was no good > standard input format that produced readable output. Every case needed > to be edited. > > So, we have to also make major changes to cirdna and lindna to support > this. > > Still, if there is enough demands from our users we can do it .... > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From golharam at umdnj.edu Fri Dec 9 18:24:24 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 09 Dec 2005 13:24:24 -0500 Subject: [EMBOSS] cirdna In-Reply-To: <41397.172.31.70.94.1134152115.squirrel@webmail.ebi.ac.uk> Message-ID: <08c801c5fced$c93b69d0$5022db82@GOLHARMOBILE1> Hi Jon, Thanks. Sure, I'll keep you informed. Right now, I'm only aware of users wanting to be able to map restriction sites in a circular piece of DNA by just inputting their DNA sequence and getting the output from cirdna. If I get anything more specific, I'll let you know. Ryan -----Original Message----- From: Jon Ison [mailto:jison at ebi.ac.uk] Sent: Friday, December 09, 2005 1:15 PM To: golharam at umdnj.edu Cc: emboss at emboss.open-bio.org Subject: Re: [EMBOSS] cirdna Hi Ryan The request is now logged which means that we'll certainly take a look at doing something for the next release. If your users have specific requirements or specification for such a program, if you forward them, they could be incorporated into any eventual design. Cheers Jon > We met with a group of our users and and there are quite a few who use > MapPlot from GCG to draw plasmids with restriction sites. Migrating > from GCG to EMBOSS means we have to provide them with alternatives to > whatever tools they used in GCG. > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd > like our users to use the web front-end (EMBOSS-Explorer by Luke > McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to > be used by EMBOSS-Explorer. If modifying cirdna is not possible, what > about incorporating TACG as a MYEMBOSS application? > > Ryan > > -----Original Message----- > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > Sent: Thursday, December 08, 2005 4:28 AM > To: emboss at emboss.open-bio.org > Cc: golharam at umdnj.edu > Subject: Re: [EMBOSS] cirdna > > > JOn Ison wrote: > >> So far as I'm aware there are no apps to generate a cirdna input >> file, > >> at least not directly. >> >> I don't think there are tools in EMBOSS to do that conversion for you >> at the moment. restrict can generate output as a report format >> but cirdna can't currently read a report format. That could change >> though. If you let us know exactly what you need we can do something >> for a future release. > > A word of caution ... I tried exactly this for cirdna and lindna a few > years ago (writing their input format as a new report format). > > Unfortunately, the font sizes and layout in cirdna and lindna did not > work in many cases - for large or small sequences there was no good > standard input format that produced readable output. Every case needed > to be edited. > > So, we have to also make major changes to cirdna and lindna to support > this. > > Still, if there is enough demands from our users we can do it .... > > regards, > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From David.Bauer at SCHERING.DE Mon Dec 12 09:54:12 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 12 Dec 2005 10:54:12 +0100 Subject: [EMBOSS] cirdna In-Reply-To: <08c801c5fced$c93b69d0$5022db82@GOLHARMOBILE1> Message-ID: What about replacing cirdna with tacg ? http://tacg.sourceforge.net/ Cheers, David. emboss-bounces at emboss.open-bio.org schrieb am 09/12/2005 19:24:24: > Hi Jon, > > Thanks. Sure, I'll keep you informed. Right now, I'm only aware of > users wanting to be able to map restriction sites in a circular piece of > DNA by just inputting their DNA sequence and getting the output from > cirdna. If I get anything more specific, I'll let you know. > > Ryan > > > -----Original Message----- > From: Jon Ison [mailto:jison at ebi.ac.uk] > Sent: Friday, December 09, 2005 1:15 PM > To: golharam at umdnj.edu > Cc: emboss at emboss.open-bio.org > Subject: Re: [EMBOSS] cirdna > > > Hi Ryan > > The request is now logged which means that we'll certainly take a look > at doing something for the next release. If your users have specific > requirements or specification for such a program, if you forward them, > they could be incorporated into any eventual design. > > Cheers > > Jon > > > > > We met with a group of our users and and there are quite a few who use > > > MapPlot from GCG to draw plasmids with restriction sites. Migrating > > from GCG to EMBOSS means we have to provide them with alternatives to > > whatever tools they used in GCG. > > > > Someone else recommended TACG (http://tacg.sourceforge.net/). We'd > > like our users to use the web front-end (EMBOSS-Explorer by Luke > > McCarthy), which means any tools must be part of EMBOSS or MYEMBOSS to > > > be used by EMBOSS-Explorer. If modifying cirdna is not possible, what > > > about incorporating TACG as a MYEMBOSS application? > > > > Ryan > > > > -----Original Message----- > > From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] > > Sent: Thursday, December 08, 2005 4:28 AM > > To: emboss at emboss.open-bio.org > > Cc: golharam at umdnj.edu > > Subject: Re: [EMBOSS] cirdna > > > > > > JOn Ison wrote: > > > >> So far as I'm aware there are no apps to generate a cirdna input > >> file, > > > >> at least not directly. > >> > >> I don't think there are tools in EMBOSS to do that conversion for you > > >> at the moment. restrict can generate output as a report format > >> but cirdna can't currently read a report format. That could change > >> though. If you let us know exactly what you need we can do something > > >> for a future release. > > > > A word of caution ... I tried exactly this for cirdna and lindna a few > > > years ago (writing their input format as a new report format). > > > > Unfortunately, the font sizes and layout in cirdna and lindna did not > > work in many cases - for large or small sequences there was no good > > standard input format that produced readable output. Every case needed > > > to be edited. > > > > So, we have to also make major changes to cirdna and lindna to support > > > this. > > > > Still, if there is enough demands from our users we can do it .... > > > > regards, > > > > Peter > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From indapa at gmail.com Mon Dec 12 21:16:56 2005 From: indapa at gmail.com (Amit Indap) Date: Mon, 12 Dec 2005 16:16:56 -0500 Subject: [EMBOSS] pasteseq Message-ID: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Hi, I'm an EMBOSS newbie but have a simple question. For the pasteseq program I'm trying to paste in the character '-' into my sequence: > pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa But my sequence is unchanged after I run the above command. However if I change insert.fa to be the sequence NN it works fine. Is there anyway I can insert the '-' character Much thanks, Amit Indap Cornell University -- Amit Indap http://www.bscb.cornell.edu/Homepages/Amit_Indap/ From pmr at ebi.ac.uk Tue Dec 13 08:46:00 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 13 Dec 2005 08:46:00 -0000 (GMT) Subject: [EMBOSS] pasteseq In-Reply-To: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Message-ID: <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> Dear Amit, > I'm an EMBOSS newbie but have a simple question. For the pasteseq > program I'm trying to paste in the character '-' into my sequence: > >> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa > > But my sequence is unchanged after I run the above command. However if > I change insert.fa to be the sequence NN it works fine. Is there > anyway I can insert the '-' character Ah ... it seems we have no program that does this easily. pasteseq is really for merging two sequences, rather than sequence editing. However, the reason pasteseq rejects your gaps is because both inputs are of type sequence and have no gaps. It makes sense to allow them. Change emboss/acd/pasteseq.acd to have the sequence input definitions below (only the types have changed) and "make install" again - or, simply copy the pasteseq.acd file to overwrite the installed one in (by default) /usr/local/share/EMBOSS/acd/pasteseq.acd We will make this change in the next release. Hope that helps, Peter ========================== section: input [ information: "Input section" type: "page" ] sequence: asequence [ parameter: "Y" type: "gapany" ] sequence: bsequence [ parameter: "Y" information: "Sequence to insert" type: "@($(acdprotein) ? gapstopprotein : gapnucleotide)" ] endsection: input From ajb at ebi.ac.uk Tue Dec 13 09:29:17 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 13 Dec 2005 09:29:17 -0000 (GMT) Subject: [EMBOSS] pasteseq In-Reply-To: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> Message-ID: <50580.81.96.70.96.1134466157.squirrel@webmail.ebi.ac.uk> Alternatively you might be able to use 'biosed'. That program will replace all occurrences of a sequence string with a replacement string. As it replaces all occurrences you need to be careful about uniqueness. So, if your sequence file (myseq.seq) was: >MYSEQ ACDEFGHI You could use the following to insert a gap at the start: biosed -target "ACDE" -replace "-ACDE" myseq.seq Alan > Hi, > > I'm an EMBOSS newbie but have a simple question. For the pasteseq > program I'm trying to paste in the character '-' into my sequence: > >> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa > > But my sequence is unchanged after I run the above command. However if > I change insert.fa to be the sequence NN it works fine. Is there > anyway I can insert the '-' character > > Much thanks, > > Amit Indap > Cornell University > > > > > > -- > Amit Indap > http://www.bscb.cornell.edu/Homepages/Amit_Indap/ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From jison at ebi.ac.uk Tue Dec 13 09:53:00 2005 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 13 Dec 2005 09:53:00 -0000 (GMT) Subject: [EMBOSS] EMBOSS Developers Course Message-ID: <40248.172.31.100.168.1134467580.squirrel@webmail.ebi.ac.uk> Hi Details on a forthcoming programming course for bioinformatics using EMBOSS are below. Apologies for the email if not interested. Please distribute to your colleagues who might be interested in this. Best regards Jon Ison The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK E-mail : jison at ebi.ac.uk BSDC 2006 Bioinformatics Software Development Course January 18-20, April 18-20 2006 Following from the popular BSDC 2003/2004 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 18-20 and April 18-20, 2006. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required to get the most out of the course, familiarity with pointers is helpful but not essential. That said, all are welcome regardless of background or experience. Places are limited and the two dates are likely to get booked up quickly so please email Liz Ford (ford at ebi.ac.uk) to register as soon as possible. We do not make a profit on the course but must charge ?125 / person (for the 3-days) to recover some of our costs. To read more about the course see http://emboss.sourceforge.net/developers/developers_course/ (1) To read more about EMBOSS see http://emboss.sourceforge.net/ To register email Liz Ford (ford at ebi.ac.uk) For further information email Jon Ison (jison at ebi.ac.uk) (1) Please note, the course is currently being revised. The course schedule is correct but details for talks & practicals are subject to change. From indapa at gmail.com Tue Dec 13 15:10:12 2005 From: indapa at gmail.com (Amit Indap) Date: Tue, 13 Dec 2005 10:10:12 -0500 Subject: [EMBOSS] pasteseq In-Reply-To: <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> References: <3cfaa4040512121316g6ef8f42at96cf99b3e873cf5e@mail.gmail.com> <1521.86.137.131.158.1134463560.squirrel@webmail.ebi.ac.uk> Message-ID: <3cfaa4040512130710l1d62777bo62dfdfb194e60ff4@mail.gmail.com> Hi Peter, Thanks for the help. I modified the pasteseq.acd file and am now able to put in gap characters. Amit Indap > Ah ... it seems we have no program that does this easily. pasteseq is > really for merging two sequences, rather than sequence editing. > > However, the reason pasteseq rejects your gaps is because both inputs are > of type sequence and have no gaps. > > It makes sense to allow them. Change emboss/acd/pasteseq.acd to have the > sequence input definitions below (only the types have changed) and "make > install" again - or, simply copy the pasteseq.acd file to overwrite the > installed one in (by default) /usr/local/share/EMBOSS/acd/pasteseq.acd > > We will make this change in the next release. > > Hope that helps, > > Peter > > ========================== > > section: input [ > information: "Input section" > type: "page" > ] > > sequence: asequence [ > parameter: "Y" > type: "gapany" > ] > > sequence: bsequence [ > parameter: "Y" > information: "Sequence to insert" > type: "@($(acdprotein) ? gapstopprotein : gapnucleotide)" > ] > > endsection: input > > > > > -- Amit Indap http://www.bscb.cornell.edu/Homepages/Amit_Indap/ From Kevin.M.Brown at asu.edu Wed Dec 14 16:18:17 2005 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 14 Dec 2005 09:18:17 -0700 Subject: [EMBOSS] CAI Tables Message-ID: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> I've searched the archives and the Net trying to find more information the list of highly-expressed genes that CAI used to create the codon tables for the various species. Does anyone know where these tables came from? From imj15 at student.canterbury.ac.nz Wed Dec 14 23:41:01 2005 From: imj15 at student.canterbury.ac.nz (Iris Vargas Jentzsch) Date: Thu, 15 Dec 2005 12:41:01 +1300 Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 Message-ID: <43A0AD8D.4050909@student.canterbury.ac.nz> Hello everybody, I need some help here. My recent tries to install EMBOSS-3.0.0 have been mostly unsuccessfull. I am working with a Fedora Core 4 Linux installation. After ./configure when I issue the command make, at the beginning it seems to work fine but it gets to some point in /pkg/EMBOSS-3.0.0/emboss/data after installing the libraries I guess, where it can?t go further. Here are the messages I get, I did cut a huge part in the middle that seemed to have no error messages (although it seemed to be the same over and over again... however if someone needs the whole long message I can post it. [root at localhost EMBOSS-3.0.0]# make Making all in plplot make[1]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' Making all in lib make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot/lib' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/plplot/lib' make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" -DEMBOSS_TOP=\"/pkg/EMBOSS-3.0.0\" -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT pdfutils.lo -MD -MP -MF ".deps/pdfutils.Tpo" -c -o pdfutils.lo pdfutils.c; \ then mv -f ".deps/pdfutils.Tpo" ".deps/pdfutils.Plo"; else rm -f ".deps/pdfutils.Tpo"; exit 1; fi mkdir .libs . . . . . gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF .deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF .deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o libnucleus.la -rpath /usr/local/lib -version-info 3:0:0 embaln.lo embcom.lo embcons.lo embdata.lo embdbi.lo embdmx.lo embdomain.lo embest.lo embexit.lo embgroup.lo embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo embmol.lo embnmer.lo embpat.lo embprop.lo embpdb.lo embread.lo embsig.lo embshow.lo embword.lo gcc -shared .libs/embaln.o .libs/embcom.o .libs/embcons.o .libs/embdata.o .libs/embdbi.o .libs/embdmx.o .libs/embdomain.o .libs/embest.o .libs/embexit.o .libs/embgroup.o .libs/embiep.o .libs/embindex.o .libs/embinit.o .libs/embmat.o .libs/embmisc.o .libs/embmol.o .libs/embnmer.o .libs/embpat.o .libs/embprop.o .libs/embpdb.o .libs/embread.o .libs/embsig.o .libs/embshow.o .libs/embword.o -Wl,-soname -Wl,libnucleus.so.3 -o .libs/libnucleus.so.3.0.0 (cd .libs && rm -f libnucleus.so.3 && ln -s libnucleus.so.3.0.0 libnucleus.so.3) (cd .libs && rm -f libnucleus.so && ln -s libnucleus.so.3.0.0 libnucleus.so) ar cru .libs/libnucleus.a embaln.o embcom.o embcons.o embdata.o embdbi.o embdmx.o embdomain.o embest.o embexit.o embgroup.o embiep.o embindex.o embinit.o embmat.o embmisc.o embmol.o embnmer.o embpat.o embprop.o embpdb.o embread.o embsig.o embshow.o embword.o ranlib .libs/libnucleus.a creating libnucleus.la (cd .libs && rm -f libnucleus.la && ln -s ../libnucleus.la libnucleus.la) make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/nucleus' Making all in emboss make[1]: Entering directory `/pkg/EMBOSS-3.0.0/emboss' Making all in acd make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/acd' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/acd' Making all in data make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' Making all in AAINDEX make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' Making all in CODONS make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' Making all in REBASE make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' Making all in PRINTS make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' Making all in PROSITE make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' make[3]: *** No rule to make target `EBLOSUMN', needed by `all-am'. Stop. make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss' make: *** [all-recursive] Error 1 I?ll appreciate very much if you can give me a hand with this. Thank you! Iris From idrummon at receptor.mgh.harvard.edu Thu Dec 15 16:10:26 2005 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Thu, 15 Dec 2005 11:10:26 -0500 Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 In-Reply-To: <43A0AD8D.4050909@student.canterbury.ac.nz> Message-ID: is it possible that you are missing some of the graphics components that are dependencies for installing emboss? does the output of the configure process show any components "not found". one way to find out if this is a problem would be to configure the emboss install without using some of the graphics components. in the configure -help for instance: --with-pngdriver=DIR root directory path of png/gd/zlib installation defaults to /usr --without-pngdriver to disable pngdriver usage completely good luck -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Nephrology Division, Massachusetts General Hospital Mailing address: Nephrology Division / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: Iris Vargas Jentzsch > Date: Thu, 15 Dec 2005 12:41:01 +1300 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4 > > Hello everybody, > > I need some help here. My recent tries to install EMBOSS-3.0.0 have been > mostly unsuccessfull. I am working with a Fedora Core 4 Linux > installation. After ./configure when I issue the command make, at the > beginning it seems to work fine but it gets to some point in > /pkg/EMBOSS-3.0.0/emboss/data after installing the libraries I guess, > where it can?t go further. Here are the messages I get, I did cut a huge > part in the middle that seemed to have no error messages (although it > seemed to be the same over and over again... however if someone needs > the whole long message I can post it. > > [root at localhost EMBOSS-3.0.0]# make > Making all in plplot > make[1]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' > Making all in lib > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot/lib' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/plplot/lib' > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot' > if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\" > -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 > -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 > -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 > -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I. -I/usr/X11R6/include > -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" > -DEMBOSS_TOP=\"/pkg/EMBOSS-3.0.0\" -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 > -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT > pdfutils.lo -MD -MP -MF ".deps/pdfutils.Tpo" -c -o pdfutils.lo pdfutils.c; \ > then mv -f ".deps/pdfutils.Tpo" ".deps/pdfutils.Plo"; else rm -f > ".deps/pdfutils.Tpo"; exit 1; fi > mkdir .libs > . > . > . > . > . > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 > -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 > -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 > -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax > -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF > .deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"3.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 > -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 > -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 > -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax > -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF > .deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1 > /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o libnucleus.la -rpath > /usr/local/lib -version-info 3:0:0 embaln.lo embcom.lo embcons.lo > embdata.lo embdbi.lo embdmx.lo embdomain.lo embest.lo embexit.lo > embgroup.lo embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo > embmol.lo embnmer.lo embpat.lo embprop.lo embpdb.lo embread.lo embsig.lo > embshow.lo embword.lo > gcc -shared .libs/embaln.o .libs/embcom.o .libs/embcons.o > .libs/embdata.o .libs/embdbi.o .libs/embdmx.o .libs/embdomain.o > .libs/embest.o .libs/embexit.o .libs/embgroup.o .libs/embiep.o > .libs/embindex.o .libs/embinit.o .libs/embmat.o .libs/embmisc.o > .libs/embmol.o .libs/embnmer.o .libs/embpat.o .libs/embprop.o > .libs/embpdb.o .libs/embread.o .libs/embsig.o .libs/embshow.o > .libs/embword.o -Wl,-soname -Wl,libnucleus.so.3 -o .libs/libnucleus.so.3.0.0 > (cd .libs && rm -f libnucleus.so.3 && ln -s libnucleus.so.3.0.0 > libnucleus.so.3) > (cd .libs && rm -f libnucleus.so && ln -s libnucleus.so.3.0.0 libnucleus.so) > ar cru .libs/libnucleus.a embaln.o embcom.o embcons.o embdata.o embdbi.o > embdmx.o embdomain.o embest.o embexit.o embgroup.o embiep.o embindex.o > embinit.o embmat.o embmisc.o embmol.o embnmer.o embpat.o embprop.o > embpdb.o embread.o embsig.o embshow.o embword.o > ranlib .libs/libnucleus.a > creating libnucleus.la > (cd .libs && rm -f libnucleus.la && ln -s ../libnucleus.la libnucleus.la) > make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/nucleus' > Making all in emboss > make[1]: Entering directory `/pkg/EMBOSS-3.0.0/emboss' > Making all in acd > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/acd' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/acd' > Making all in data > make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' > Making all in AAINDEX > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX' > Making all in CODONS > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS' > Making all in REBASE > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE' > Making all in PRINTS > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS' > Making all in PROSITE > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE' > make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[3]: *** No rule to make target `EBLOSUMN', needed by `all-am'. Stop. > make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss' > make: *** [all-recursive] Error 1 > > > I?ll appreciate very much if you can give me a hand with this. Thank you! > > Iris > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Tue Dec 20 10:18:17 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Dec 2005 10:18:17 +0000 Subject: [EMBOSS] CAI Tables In-Reply-To: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> Message-ID: <43A7DA69.2040405@ebi.ac.uk> Kevin Brown wrote: > I've searched the archives and the Net trying to find more information > the list of highly-expressed genes that CAI used to create the codon > tables for the various species. Does anyone know where these tables > came from? Well, it is a long story ... The original CAI (Codon Adaptation Index) was calculated for S. cerevisiae and used a set of 24 genes (ribosomal proteins, for example) that were known to be highly expressed. Many years ago when I wrote a program to calculate the codon usage for S. pombe (fission yeast) in a program called "codfish", I created a table for the few S. pombe genes from the same set that had already been sequenced. On arriving at the Sanger Centre, where they were sequencing a lot of S. cerevisiae, I needed the codon usage table for the original CAI - and found that when I used the current gene sequences I got the wrong answer. After some tweaking I was able to reconstruct the original versions of the cerevisiae sequences and could reproduce the "standard" CAI values. The differences were minor - mainly missed short 5' exons. The tables Eyeast_cai.cod and Eschpo_cai.cut are the result of these two tables. There are, for historic reasons, copies of these tables with no headers and different names which are "obsolete" and will disappear in EMBOSS 4.0.0. As for "codfish" ... it implemented an algorithm from Frank Wright to calculate the effective number of codons. Frank is a vegan (does not eat codfish), so in EMBOSS we renamed it "chips" :-) Hope that helps! Peter From hegedus at biomembrane.hu Tue Dec 20 13:17:18 2005 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Tue, 20 Dec 2005 08:17:18 -0500 Subject: [EMBOSS] CAI Tables In-Reply-To: <43A7DA69.2040405@ebi.ac.uk> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> <43A7DA69.2040405@ebi.ac.uk> Message-ID: <43A8045E.1050905@biomembrane.hu> Hi, I am not a CAI expert; I also could not find one around me; reading was not enough for me in this topic. So I would like to take the opportunity to ask a CAI (not EMBOSS) related question. What can you tell me about human (mammalian) CAI tables? What do you think/know about the FOP values introduced by Lavner & Kotlar? http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15716084&query_hl=1 I would like to use some measure to predict the translation speed of certain regions in some proteins I am interested in. Thanks, Tamas Peter Rice wrote: > Kevin Brown wrote: > > >>I've searched the archives and the Net trying to find more information >>the list of highly-expressed genes that CAI used to create the codon >>tables for the various species. Does anyone know where these tables >>came from? > > > Well, it is a long story ... > > The original CAI (Codon Adaptation Index) was calculated for S. cerevisiae and > used a set of 24 genes (ribosomal proteins, for example) that were known to be > highly expressed. > > Many years ago when I wrote a program to calculate the codon usage for S. > pombe (fission yeast) in a program called "codfish", I created a table for the > few S. pombe genes from the same set that had already been sequenced. > > On arriving at the Sanger Centre, where they were sequencing a lot of S. > cerevisiae, I needed the codon usage table for the original CAI - and found > that when I used the current gene sequences I got the wrong answer. > > After some tweaking I was able to reconstruct the original versions of the > cerevisiae sequences and could reproduce the "standard" CAI values. The > differences were minor - mainly missed short 5' exons. > > The tables Eyeast_cai.cod and Eschpo_cai.cut are the result of these two > tables. There are, for historic reasons, copies of these tables with no > headers and different names which are "obsolete" and will disappear in EMBOSS > 4.0.0. > > As for "codfish" ... it implemented an algorithm from Frank Wright to > calculate the effective number of codons. Frank is a vegan (does not eat > codfish), so in EMBOSS we renamed it "chips" :-) > > Hope that helps! > > Peter > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From pmr at ebi.ac.uk Tue Dec 20 13:59:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Dec 2005 13:59:00 +0000 Subject: [EMBOSS] CAI Tables In-Reply-To: <43A8045E.1050905@biomembrane.hu> References: <1A4207F8295607498283FE9E93B775B4B2838F@EX02.asurite.ad.asu.edu> <43A7DA69.2040405@ebi.ac.uk> <43A8045E.1050905@biomembrane.hu> Message-ID: <43A80E24.20008@ebi.ac.uk> Tamas Hegedus wrote: > Hi, > > I am not a CAI expert; I also could not find one around me; reading was > not enough for me in this topic. > So I would like to take the opportunity to ask a CAI (not EMBOSS) > related question. > > What can you tell me about human (mammalian) CAI tables? > What do you think/know about the FOP values introduced by Lavner & Kotlar? > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15716084&query_hl=1 > > > I would like to use some measure to predict the translation speed of > certain regions in some proteins I am interested in. Well, I am not really a CAI expert either. I hope there is someone better informed who can help. I do like the "unaffected by amino acid composition" part of their statistic, but that may be just my bias. If this statistic would be useful, we can try to implement it in EMBOSS. Any opinions? regards, Peter From golharam at umdnj.edu Wed Dec 21 18:45:48 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 21 Dec 2005 13:45:48 -0500 Subject: [EMBOSS] EDNAFULL Message-ID: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> Does anyone know know how EDNAFULL was derived? Ie, How were the scores it uses determined? Google Scholar didn't turn anything up and I'm not finding anything in the EMBOSS documentation... Ryan From pmr at ebi.ac.uk Thu Dec 22 09:02:34 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 22 Dec 2005 09:02:34 -0000 (GMT) Subject: [EMBOSS] EDNAFULL In-Reply-To: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> References: <00b801c6065e$c2c6d1a0$2f01a8c0@GOLHARMOBILE1> Message-ID: <1376.86.137.131.158.1135242154.squirrel@webmail.ebi.ac.uk> Ryan Golhar writes: > Does anyone know know how EDNAFULL was derived? Ie, How were the scores > it uses determined? > > Google Scholar didn't turn anything up and I'm not finding anything in > the EMBOSS documentation... We should add more information to the header in the matrix file. Will do for the next release. The DNA matrices are simply the ones supplied by NCBI in ftp://ftp.ncbi.nih.gov/blast/matrices/ as files NUC4.2 (EDNAMAT) and NUC4.4 (EDNAFULL). NUC4.2 simply scores 5 for a match, and -4 for a mismatch. NUC4.4 scores 5 for a match, but provides appropriate scores for ambiguity codes so that, for example, R:A scores +1 (rounded up average of -4, -4, 5, 5) The matrices were created by Todd Lowe in 1992. I am not sure where Todd was working at that time. Hope that helps, Peter Rice From ajb at ebi.ac.uk Fri Dec 23 08:45:35 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 23 Dec 2005 08:45:35 -0000 (GMT) Subject: [EMBOSS] Updated dbx* applications Message-ID: <52044.81.96.70.96.1135327535.squirrel@webmail.ebi.ac.uk> These applications have been rewritten to cope with an unlimited number of duplicates (e.g. EMBL WGS file accession numbers). The replacement files are now on our ftp server. ftp://emboss.open-bio.org:/pub/EMBOSS/fixes/ Look at the README file in that directory to see which files you need. Some speed-ups have also been added and the programs now honour the directory settings in emboss.default. Alan