[Bioperl-l] cdd-search with remoteblast?
Cook, Malcolm
MEC at stowers.org
Tue Jul 14 14:33:46 EDT 2009
Jonas,
I'm glad to hear it works for you too.
I noted the recipe for success here: http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast#Status
Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri
> -----Original Message-----
> From: Jonas Schaer [mailto:Brotelzwieb at gmx.de]
> Sent: Tuesday, July 14, 2009 12:05 PM
> To: Cook, Malcolm; Chris Fields
> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
>
> Hi chris and malcom,
> seems to work here, too. thank u both a lot. great job :)
> best regards, jonas
> ----- Original Message -----
> From: "Chris Fields" <cjfields1 at gmail.com>
> To: "Cook, Malcolm" <MEC at stowers.org>
> Cc: "'Jonas Schaer'" <Brotelzwieb at gmx.de>; "'BioPerl List'"
> <bioperl-l at lists.open-bio.org>
> Sent: Friday, July 10, 2009 8:04 PM
> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
>
>
> > Malcolm,
> >
> > Nice! Go ahead and add the test in; we can look at trying to get
> > CDD_SEARCH working at some point but this is a nice workaround.
> >
> > chris
> >
> > On Jul 10, 2009, at 10:45 AM, Cook, Malcolm wrote:
> >
> >> Chris, I've added a test to bioperl RemoteBlast.t that demonstrates
> >> the following. Is it appropriate to submit it?
> >>
> >> Jonas, OK, I was a little quick on the gun... but I've got it now.
> >>
> >> You don't need to change the wrapper. Here is what you need to do:
> >>
> >> # 1) set your database like this:
> >>
> >> -database => 'cdsearch/cdd', # c.f.
> >>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html
> >> for other cdd database options
> >>
> >> # 2) add this line before submitting the job:
> >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
> >>
> >> You're in - No other changes needed.
> >>
> >> Malcolm Cook
> >> Stowers Institute for Medical Research - Kansas City, Missouri
> >>
> >>
> >>> -----Original Message-----
> >>> From: Jonas Schaer [mailto:Brotelzwieb at gmx.de]
> >>> Sent: Friday, July 10, 2009 4:18 AM
> >>> To: BioPerl List; Cook, Malcolm; Chris Fields
> >>> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
> >>>
> >>> Hi,
> >>> I tried to do what Malcom proposed my ($prog = 'rpsblast';
> >>> my $db =
> >>> 'CDD';) but that didn't work.
> >>>
> >>> ------------- EXCEPTION: Bio::Root::Exception -------------
> >>> MSG: Value rpsblast for PUT parameter PROGRAM does not match
> >>> expression t?blast[ pnx]. Rejecting.
> >>> STACK: Error::throw
> >>> STACK: Bio::Root::Root::throw
> C:/Perl/site/lib/Bio/Root/Root.pm:359
> >>> STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
> >>> C:/Perl/site/lib/Bio/Tools
> >>> /Run/RemoteBlast.pm:329
> >>> STACK: Bio::Tools::Run::RemoteBlast::new
> >>> C:/Perl/site/lib/Bio/Tools/Run/RemoteBl
> >>> ast.pm:257
> >>> STACK: blast_a_seq2.pm:14
> >>> -----------------------------------------------------------
> >>> So I should try to "change the wrapper to allow 'rpsblast'",
> >>> right? Could You tell me how to do that, please? So sorry but
> >>> I have no idea yet...:) If that doesn't work, is there any
> >>> other way to run cdd-searches with perl?
> >>> Thank you so much!
> >>> Regards, Jonas
> >>>
> >>> ----- Original Message -----
> >>> From: "Chris Fields" <cjfields1 at gmail.com>
> >>> To: "Cook, Malcolm" <MEC at stowers.org>
> >>> Cc: "'Jonas Schaer'" <Brotelzwieb at gmx.de>; "'BioPerl List'"
> >>> <bioperl-l at lists.open-bio.org>; "'Smithies, Russell'"
> >>> <Russell.Smithies at agresearch.co.nz>; <cjfields at bioperl.org>
> >>> Sent: Thursday, July 09, 2009 9:19 PM
> >>> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
> >>>
> >>>
> >>>> I've scheduled this tentatively for the 1.6 release
> series (just not
> >>>> sure when yet). It may work as is, but I haven't tried
> it out yet
> >>>> (and am hazarding to guess it only retrieves the single
> main RID at
> >>>> the moment).
> >>>>
> >>>> chris
> >>>>
> >>>> On Jul 9, 2009, at 10:56 AM, Cook, Malcolm wrote:
> >>>>
> >>>>> Jonas,
> >>>>>
> >>>>> If you want to continue to use the bioperl remoteblast
> interface,
> >>>>> probably what you should do is simply call it twice.
> >>>>>
> >>>>> Once, as you already know how to do, which will return
> without CDD
> >>>>> results.
> >>>>>
> >>>>> Secondly, to get the CDD results, call remoteblast a
> second time.
> >>>>> This time, using
> >>>>> -database => 'CDD'
> >>>>> -program => 'rpsblast'
> >>>>>
> >>>>> However, the wrapper may object to the 'rpsblast'
> program. It is
> >>>>> not listed in the POD -
> >>>>>
> >>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/Tools/Run/R
> >>> emoteBlast.pm)
> >>>>> If so, my guess is that changing the perl wrapper to allow
> >>>>> rpsblast will "just work" (tm). I've cc:ed
> >>> cjfields at bioperl.org for
> >>>>> his opinion on this.
> >>>>>
> >>>>> Also, you might want to perform the CDD search first,
> especially if
> >>>>> you are streaming results to eyeball that might like
> something to
> >>>>> look at while the second (presumably longer) search is running.
> >>>>>
> >>>>> Cheers,
> >>>>>
> >>>>> Malcolm Cook
> >>>>> Stowers Institute for Medical Research - Kansas City, Missouri
> >>>>>
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: bioperl-l-bounces at lists.open-bio.org
> >>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> >>>>>> Jonas Schaer
> >>>>>> Sent: Thursday, July 09, 2009 5:16 AM
> >>>>>> To: BioPerl List; Smithies, Russell
> >>>>>> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
> >>>>>>
> >>>>>> Hi guys,
> >>>>>> Thank you all so much for your help and patience :). Of
> >>>>>> course you were right and I finaly found the right
> >>>>>> put-parameter to get exactly the same hits as on the homepage.
> >>>>>> I do have an other question though :)...
> >>>>>> I now want to include a search for conserved domains, but
> >>>>>> when I try to use the CDD_SEARCH-parameter
> >>>>>> (http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node16.html#
> >>>>>> sub:CDD_SEARCH)
> >>>>>> like the other put-parameters the way chris once told
> >>>>>> me(works fine with the other params):
> >>>>>>
> >>>>>> my %put = (
> >>>>>> WORD_SIZE => 3,
> >>>>>> HITLIST_SIZE => 100,
> >>>>>> THRESHOLD => 11,
> >>>>>> FILTER => 'R',
> >>>>>> GENETIC_CODE => 1,
> >>>>>> CDD_SEARCH => 'on'
> >>>>>> ###I tried it
> >>>>>> with 'true' and '1', too.
> >>>>>>
> >>>>>> );
> >>>>>>
> >>>>>> for my $putName (keys %put) {
> >>>>>> $factory->submit_parameter($putName,$put{$putName});
> >>>>>> }
> >>>>>>
> >>>>>>
> >>>>>> ...an exception is thrown:
> >>>>>>
> >>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
> >>>>>> MSG: CDD_SEARCH is not a valid PUT parameter.
> >>>>>> STACK: Error::throw
> >>>>>> STACK: Bio::Root::Root::throw
> >>> C:/Perl/site/lib/Bio/Root/Root.pm:359
> >>>>>> STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
> >>>>>> C:/Perl/site/lib/Bio/Tools
> >>>>>> /Run/RemoteBlast.pm:325
> >>>>>> STACK: main::blast_a_sequence firsteval0.8.pm:383
> >>>>>> STACK: main::blast_it firsteval0.8.pm:288
> >>>>>> STACK: firsteval0.8.pm:35
> >>>>>> ----------------------------------------------------------- .
> >>>>>> I guess somehow this could be the solution to my problem:
> >>>>>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node78.html#s
> >>>>>> ub:RID-for-Simultaneous
> >>>>>> , but unfortunately I don't understand what to do.
> >>>>>> I'm so sorry to bother you with this but please help me once
> >>>>>> more...:)
> >>>>>>
> >>>>>> Best regards and thanks in advance,
> >>>>>> Jonas
> >>>>>>
> >>>>>> ----- Original Message -----
> >>>>>> From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
> >>>>>> To: "'Jonas Schaer'" <Brotelzwieb at gmx.de>
> >>>>>> Cc: "'Chris Fields'" <cjfields at illinois.edu>; "'BioPerl List'"
> >>>>>> <bioperl-l at lists.open-bio.org>
> >>>>>> Sent: Monday, July 06, 2009 10:56 PM
> >>>>>> Subject: RE: [Bioperl-l] different results with
> >>> remote-blast skript
> >>>>>>
> >>>>>>
> >>>>>> Hi Jonas,
> >>>>>> You can't just play with the BLAST parameters and hope
> >>> for a "better"
> >>>>>> result.
> >>>>>> I'd suggest that if you aren't sure what they do, you should
> >>>>>> leave them
> >>>>>> alone as small changes can make huge differences in the
> >>>>>> output - it's quite
> >>>>>> possible to miss finding what you're looking for by using
> >>> the wrong
> >>>>>> parameters.
> >>>>>> If all else fails, read the blast manual:
> >>>>>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall
> >>>>>> _all.html
> >>>>>> http://www.ncbi.nlm.nih.gov/blast/tutorial/
> >>>>>> Or Read Ian Korfs' excellent book:
> >>>>>> http://books.google.com/books?id=xvcnhDG9fNUC&lpg=PR17&ots=WJp
> >>>>> fuHF6Hn&dq=ian%20korf%20%20blast%20book&pg=PA3
> >>>>>>
> >>>>>> Don't worry about the integer overflow bug as there's nothing
> >>>>>> you can do
> >>>>>> about it. If you're interested, Google and Wikipedia are your
> >>>>>> friends:
> >>>>>> http://en.wikipedia.org/wiki/Integer_overflow
> >>>>>>
> >>>>>>
> >>>>>> Russell
> >>>>>>
> >>>>>>> -----Original Message-----
> >>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>>>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
> >>>>>>> Sent: Tuesday, 7 July 2009 12:14 a.m.
> >>>>>>> To: BioPerl List; Chris Fields
> >>>>>>> Subject: Re: [Bioperl-l] different results with
> >>> remote-blast skript
> >>>>>>>
> >>>>>>> Hi guys, thanks for your answers so far.
> >>>>>>> @jason: integer overflow in blast.... sorry, but what do
> >>>>>> you mean by that?
> >>>>>>> how can I fix it...?
> >>>>>>>
> >>>>>>> Since I never really changed any parameters I thought them
> >>>>>> all to be
> >>>>>>> default.
> >>>>>>> whatever, I tried to get "better" results with my prog
> >>> by changing
> >>>>>>> these:
> >>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
> >>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
> >>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
> >>>>>>>
> >>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATI
> >>>>>> STICS'} =
> >>>>>>> '1';
> >>>>>>> with no effect...I guess these were default values anyway.
> >>>>>>>
> >>>>>>> So please maybe you can tell me all the other parameters I
> >>>>>> can change with
> >>>>>>> my
> >>>>>>> perl-skript AND how to do that?
> >>>>>>> Unfortunately both, perl and the blast-algorithm are pretty
> >>>>>> much new to
> >>>>>>> me,
> >>>>>>> maybe thats why I just cannot find out how to do that on my
> >>>>>> own... :/
> >>>>>>>
> >>>>>>> Here is the output I get with my remote-blast skript:
> >>>>>>>
> >>>>>> ##############################################################
> >>>>>> ################
> >>>>>>> ###################################
> >>>>>>> Query Name:
> >>>>>>>
> >>>
> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSL
> >>>>>>> L
> >>>>>>> hit name is ref|XP_001702807.1|
> >>>>>>> score is 442
> >>>>>>> BLASTP 2.2.21+
> >>>>>>> Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
> >>>>>> A. Schaffer,
> >>>>>>> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
> >>>>>> Lipman (1997),
> >>>>>>> "Gapped
> >>>>>>> BLAST and PSI-BLAST: a new generation of protein
> database search
> >>>>>>> programs",
> >>>>>>> Nucleic Acids Res. 25:3389-3402.
> >>>>>>>
> >>>>>>>
> >>>>>>> Reference for composition-based statistics: Alejandro A.
> >>>>>>> Schaffer, L. Aravind, Thomas L. Madden, Sergei Shavirin,
> >>>>>> John L. Spouge,
> >>>>>>> Yuri
> >>>>>>> I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
> >>>>>> "Improving the
> >>>>>>> accuracy of PSI-BLAST protein database searches with
> >>>>>> composition-based
> >>>>>>> statistics and other refinements", Nucleic Acids Res.
> >>> 29:2994-3005.
> >>>>>>>
> >>>>>>>
> >>>>>>> RID: 53STX5G2013
> >>>>>>>
> >>>>>>>
> >>>>>>> Database: All non-redundant GenBank CDS
> >>>>>>> translations+PDB+SwissProt+PIR+PRF excluding
> >>> environmental samples
> >>>>>>> from WGS projects
> >>>>>>> 9,252,587 sequences; 3,169,972,781 total
> letters Query=
> >>>>>>>
> >>>>>>
> >>>
> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSLL
> >>>>>>>
> >>>>>>
> >>>
> DVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDNAFRQAHQNTAM
> >>>>>>> ATGPDPDDEYE
> >>>>>>> Length=150
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>> Score
> >>>>>>> E
> >>>>>>> Sequences producing significant alignments:
> >>>>>> (Bits)
> >>>>>>> Value
> >>>>>>>
> >>>>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> >>>>>> reinhard... 174
> >>>>>>> 2e-42
> >>>>>>>
> >>>>>>>
> >>>>>>> ALIGNMENTS
> >>>>>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> >>> reinhardtii]
> >>>>>>> gb|EDP06586.1| ClpS-like protein [Chlamydomonas reinhardtii]
> >>>>>>> Length=303
> >>>>>>>
> >>>>>>> Score = 174 bits (442), Expect = 2e-42, Method:
> >>>>>> Composition-based
> >>>>>>> stats.
> >>>>>>> Identities = 150/150 (100%), Positives = 150/150 (100%),
> >>>>>> Gaps = 0/150
> >>>>>>> (0%)
> >>>>>>>
> >>>>>>> Query 1
> >>>>>> MGSSSVGTYHLLLVLMgaggeqqavqagaevaSTEQVDGSGMAANSRGSTSGSEQPPrds
> >>>>>>> 60
> >>>>>>>
> >>>>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
> >>>>>>> Sbjct 154
> >>>>>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
> >>>>>>> 213
> >>>>>>>
> >>>>>>> Query 61
> >>>>>> dlgllrslldVAGVDRTalevkllalaeagaeMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>>>>> 120
> >>>>>>>
> >>>>>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>>>>> Sbjct 214
> >>>>>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>>>>> 273
> >>>>>>>
> >>>>>>> Query 121 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 150
> >>>>>>> AWHERDDNAFRQAHQNTAMATGPDPDDEYE
> >>>>>>> Sbjct 274 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 303
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Database: All non-redundant GenBank CDS
> >>>>>>> translations+PDB+SwissProt+PIR+PRF
> >>>>>>> excluding environmental samples from WGS projects
> >>>>>>> Posted date: Jul 5, 2009 4:41 AM
> >>>>>>> Number of letters in database: -1,124,994,511
> >>>>>>> Number of sequences in database: 9,252,587
> >>>>>>>
> >>>>>>> Lambda K H
> >>>>>>> 0.309 0.122 0.345
> >>>>>>> Gapped
> >>>>>>> Lambda K H
> >>>>>>> 0.267 0.0410 0.140
> >>>>>>> Matrix: BLOSUM62
> >>>>>>> Gap Penalties: Existence: 11, Extension: 1
> >>>>>>> Number of Sequences: 9252587
> >>>>>>> Number of Hits to DB: 60273703
> >>>>>>> Number of extensions: 1448367
> >>>>>>> Number of successful extensions: 2103
> >>>>>>> Number of sequences better than 10: 0
> >>>>>>> Number of HSP's better than 10 without gapping: 0
> >>>>>>> Number of HSP's gapped: 2113
> >>>>>>> Number of HSP's successfully gapped: 0
> >>>>>>> Length of query: 150
> >>>>>>> Length of database: 3169972781
> >>>>>>> Length adjustment: 113
> >>>>>>> Effective length of query: 37
> >>>>>>> Effective length of database: 2124430450
> >>>>>>> Effective search space: 78603926650
> >>>>>>> Effective search space used: 78603926650
> >>>>>>> T: 11
> >>>>>>> A: 40
> >>>>>>> X1: 16 (7.1 bits)
> >>>>>>> X2: 38 (14.6 bits)
> >>>>>>> X3: 64 (24.7 bits)
> >>>>>>> S1: 42 (20.8 bits)
> >>>>>>> S2: 74 (33.1 bits)
> >>>>>>>
> >>>>>>>
> >>>>>> ##############################################################
> >>>>>> ################
> >>>>>>> ###################################
> >>>>>>> and here are the hits (?) of the blast-algorithm on the
> >>>>>> ncbi-homepage with
> >>>>>>> the same query of course:
> >>>>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> >>>>>> reinhard... 300
> >>>>>>> 3e-80
> >>>>>>> ref|XP_001942719.1| PREDICTED: similar to GA16705-PA
> >>>>>> [Acyrtho... 36.2
> >>>>>>> 1.1
> >>>>>>> ref|ZP_03781446.1| hypothetical protein RUMHYD_00880
> >>>>>> [Blautia... 35.4
> >>>>>>> 1.8
> >>>>>>> ref|XP_001563232.1| leucyl-tRNA synthetase [Leishmania
> >>>>>> brazil... 34.3
> >>>>>>> 4.2
> >>>>>>> ref|XP_680841.1| hypothetical protein AN7572.2
> >>>>>> [Aspergillus n... 33.5
> >>>>>>> 6.0
> >>>>>>> ref|YP_001768110.1| hypothetical protein M446_1150
> >>>>>> [Methyloba... 33.5
> >>>>>>> 7.0
> >>>>>>>
> >>>>>> ##############################################################
> >>>>>> ################
> >>>>>>> ###################################at
> >>>>>>> least the first hit is the same, but even there there is a
> >>>>>> different score
> >>>>>>> and e-value.
> >>>>>>>
> >>>>>>> thanks so much for any help :)
> >>>>>>> regards, jonas
> >>>>>>>
> >>>>>>>
> >>>>>>> ----- Original Message -----
> >>>>>>> From: "Chris Fields" <cjfields at illinois.edu>
> >>>>>>> To: "Jason Stajich" <jason at bioperl.org>
> >>>>>>> Cc: "Smithies, Russell"
> >>>>>> <Russell.Smithies at agresearch.co.nz>; "'BioPerl
> >>>>>>> List'" <bioperl-l at lists.open-bio.org>; "'Jonas Schaer'"
> >>>>>>> <Jonas_Schaer at gmx.de>
> >>>>>>> Sent: Monday, July 06, 2009 12:51 AM
> >>>>>>> Subject: Re: [Bioperl-l] different results with
> >>> remote-blast skript
> >>>>>>>
> >>>>>>>
> >>>>>>>> That inspires confidence ;>
> >>>>>>>>
> >>>>>>>> chris
> >>>>>>>>
> >>>>>>>> On Jul 5, 2009, at 4:40 PM, Jason Stajich wrote:
> >>>>>>>>
> >>>>>>>>> integer overflow in blast....
> >>>>>>>>>
> >>>>>>>>> On Jul 5, 2009, at 2:00 PM, Smithies, Russell wrote:
> >>>>>>>>>
> >>>>>>>>>> I'd guess it's a difference in the parameters used.
> >>>>>>>>>> Interesting that both have the number of letters
> in the db as
> >>>>>>>>>> "-1,125,070,205", I assume that's a bug :-)
> >>>>>>>>>>
> >>>>>>>>>> Stats from your remote_blast:
> >>>>>>>>>>
> >>>>>>>>>> 'stats' => {
> >>>>>>>>>> 'S1' => '42',
> >>>>>>>>>> 'S1_bits' => '20.8',
> >>>>>>>>>> 'lambda' => '0.309',
> >>>>>>>>>> 'entropy' => '0.345',
> >>>>>>>>>> 'kappa_gapped' => '0.0410',
> >>>>>>>>>> 'T' => '11',
> >>>>>>>>>> 'kappa' => '0.122',
> >>>>>>>>>> 'X3_bits' => '24.7',
> >>>>>>>>>> 'X1' => '16',
> >>>>>>>>>> 'lambda_gapped' => '0.267',
> >>>>>>>>>> 'X2' => '38',
> >>>>>>>>>> 'S2' => '74',
> >>>>>>>>>> 'seqs_better_than_cutoff' => '0',
> >>>>>>>>>> 'posted_date' => 'Jul 4, 2009 4:41 AM',
> >>>>>>>>>> 'Hits_to_DB' => '60102303',
> >>>>>>>>>> 'dbletters' => '-1125070205',
> >>>>>>>>>> 'A' => '40',
> >>>>>>>>>> 'num_successful_extensions' => '2004',
> >>>>>>>>>> 'num_extensions' => '1436892',
> >>>>>>>>>> 'X1_bits' => '7.1',
> >>>>>>>>>> 'X3' => '64',
> >>>>>>>>>> 'entropy_gapped' => '0.140',
> >>>>>>>>>> 'dbentries' => '9252258',
> >>>>>>>>>> 'X2_bits' => '14.6',
> >>>>>>>>>> 'S2_bits' => '33.1'
> >>>>>>>>>> }
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Stats from a blast done on the NCBI webpage:
> >>>>>>>>>>
> >>>>>>>>>> Database: All non-redundant GenBank CDS
> >>>>>> translations+PDB+SwissProt
> >>>>>>>>>> +PIR+PRF
> >>>>>>>>>> excluding environmental samples from WGS projects
> >>>>>>>>>> Posted date: Jul 4, 2009 4:41 AM
> >>>>>>>>>> Number of letters in database: -1,125,070,205
> >>>>>>>>>> Number of sequences in database: 9,252,258
> >>>>>>>>>>
> >>>>>>>>>> Lambda K H
> >>>>>>>>>> 0.309 0.124 0.340
> >>>>>>>>>> Gapped
> >>>>>>>>>> Lambda K H
> >>>>>>>>>> 0.267 0.0410 0.140
> >>>>>>>>>> Matrix: BLOSUM62
> >>>>>>>>>> Gap Penalties: Existence: 11, Extension: 1
> >>>>>>>>>> Number of Sequences: 9252258
> >>>>>>>>>> Number of Hits to DB: 86493230
> >>>>>>>>>> Number of extensions: 3101413
> >>>>>>>>>> Number of successful extensions: 9001
> >>>>>>>>>> Number of sequences better than 100: 65
> >>>>>>>>>> Number of HSP's better than 100 without gapping: 0
> >>>>>>>>>> Number of HSP's gapped: 9000
> >>>>>>>>>> Number of HSP's successfully gapped: 66
> >>>>>>>>>> Length of query: 150
> >>>>>>>>>> Length of database: 3169897087
> >>>>>>>>>> Length adjustment: 113
> >>>>>>>>>> Effective length of query: 37
> >>>>>>>>>> Effective length of database: 2124391933
> >>>>>>>>>> Effective search space: 78602501521
> >>>>>>>>>> Effective search space used: 78602501521
> >>>>>>>>>> T: 11
> >>>>>>>>>> A: 40
> >>>>>>>>>> X1: 16 (7.1 bits)
> >>>>>>>>>> X2: 38 (14.6 bits)
> >>>>>>>>>> X3: 64 (24.7 bits)
> >>>>>>>>>> S1: 42 (20.8 bits)
> >>>>>>>>>> S2: 65 (29.6 bits)
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> -----Original Message-----
> >>>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-
> >>>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
> >>>>>>>>>>> Sent: Sunday, 28 June 2009 10:15 p.m.
> >>>>>>>>>>> To: BioPerl List
> >>>>>>>>>>> Subject: [Bioperl-l] different results with
> >>> remote-blast skript
> >>>>>>>>>>>
> >>>>>>>>>>> Hi again :)
> >>>>>>>>>>> please, I only have this little question:
> >>>>>>>>>>> why do I get different results with my remote::blast
> >>>>>> perl skript
> >>>>>>>>>>> then on the
> >>>>>>>>>>> ncbi blast homepage?
> >>>>>>>>>>> I am using blastp, the query is an amino-sequence
> (different
> >>>>>>>>>>> results with any
> >>>>>>>>>>> sequence, differences not only in number of hits but
> >>> even in e-
> >>>>>>>>>>> values, scores
> >>>>>>>>>>> etc...), the database is 'nr'.
> >>>>>>>>>>> PLEASE help me,
> >>>>>>>>>>> thank you in advance,
> >>>>>>>>>>> Jonas
> >>>>>>>>>>>
> >>>>>>>>>>> ps: my skript:
> >>>>>>>>>>>
> >>>>>>>
> >>>>>> ##############################################################
> >>>>>> ################
> >>>>>>>>>>> ##
> >>>>>>>>>>> use Bio::Seq::SeqFactory;
> >>>>>>>>>>> use Bio::Tools::Run::RemoteBlast;
> >>>>>>>>>>> use strict;
> >>>>>>>>>>> my @blast_report;
> >>>>>>>>>>> my $prog = 'blastp';
> >>>>>>>>>>> my $db = 'nr';
> >>>>>>>>>>> my $e_val= '1e-10';
> >>>>>>>>>>> #my $e_val= '10';
> >>>>>>>>>>> my @params = ( '-prog' => $prog,
> >>>>>>>>>>> '-data' => $db,
> >>>>>>>>>>> '-expect' => $e_val,
> >>>>>>>>>>> '-readmethod' => 'SearchIO' );
> >>>>>>>>>>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >>>>>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'}
> = '11 1';
> >>>>>>>>>>>
> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
> >>>>>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
> >>>>>>>>>>> $
> >>>>>>>>>>> Bio
> >>>>>>>>>>>
> >>>>>>
> ::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'}
> >>>>>>>>>>> = '1';
> >>>>>>>>>>>
> >>>>>>>>>>> my
> >>>>>>>>>>> $
> >>>>>>>>>>> blast_seq
> >>>>>>>>>>>
> >>>>>>
> >>>
> ='MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLR
> >>>>>>>>>>>
> >>>>>>>
> >>>>>> SLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDN
> >>>>>> AFRQAHQNTAMATGPD
> >>>>>>>>>>> PDDEYE';
> >>>>>>>>>>> #$v is just to turn on and off the messages
> >>>>>>>>>>> my $v = 1;
> >>>>>>>>>>> my $seqbuilder = Bio::Seq::SeqFactory->new('-type' =>
> >>>>>>>>>>> 'Bio::PrimarySeq');
> >>>>>>>>>>> my $seq = $seqbuilder->create(-seq =>$blast_seq,
> >>> -display_id =>
> >>>>>>>>>>> "$blast_seq");
> >>>>>>>>>>> my $filename='temp2.out';
> >>>>>>>>>>> my $r = $factory->submit_blast($seq);
> >>>>>>>>>>> print STDERR "waiting..." if( $v > 0 );
> >>>>>>>>>>> while ( my @rids = $factory->each_rid )
> >>>>>>>>>>> {
> >>>>>>>>>>> foreach my $rid ( @rids )
> >>>>>>>>>>> {
> >>>>>>>>>>> my $rc = $factory->retrieve_blast($rid);
> >>>>>>>>>>> if( !ref($rc) )
> >>>>>>>>>>> {
> >>>>>>>>>>> if( $rc < 0 )
> >>>>>>>>>>> {
> >>>>>>>>>>> $factory->remove_rid($rid);
> >>>>>>>>>>> }
> >>>>>>>>>>> print STDERR "." if ( $v > 0 );
> >>>>>>>>>>> }
> >>>>>>>>>>> else
> >>>>>>>>>>> {
> >>>>>>>>>>> my $result = $rc->next_result();
> >>>>>>>>>>> $factory->save_output($filename);
> >>>>>>>>>>> $factory->remove_rid($rid);
> >>>>>>>>>>> print "\nQuery Name: ",
> >>>>>> $result->query_name(),
> >>>>>>>>>>> "\n";
> >>>>>>>>>>> while ( my $hit = $result->next_hit )
> >>>>>>>>>>> {
> >>>>>>>>>>> next unless ( $v > 0);
> >>>>>>>>>>> print "\thit name is ",
> >>> $hit->name, "\n";
> >>>>>>>>>>> while( my $hsp = $hit->next_hsp )
> >>>>>>>>>>> {
> >>>>>>>>>>> print "\t\tscore is ",
> >>>>>> $hsp->score, "\n";
> >>>>>>>>>>> }
> >>>>>>>>>>> }
> >>>>>>>>>>> }
> >>>>>>>>>>> }
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> }
> >>>>>>>>>>> @blast_report = get_file_data ($filename);
> >>>>>>>>>>> return @blast_report;
> >>>>>>>>>>>
> >>>>>>>
> >>>>>> ##############################################################
> >>>>>> ################
> >>>>>>>>>>> ####
> >>>>>>>>>>> _______________________________________________
> >>>>>>>>>>> Bioperl-l mailing list
> >>>>>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>>> =
> >>>>>>>>>> =
> >>>>>>>>>>
> >>>>>>
> >>>
> =====================================================================
> >>>>>>>>>> Attention: The information contained in this message and/or
> >>>>>>>>>> attachments
> >>>>>>>>>> from AgResearch Limited is intended only for the
> >>>>>> persons or entities
> >>>>>>>>>> to which it is addressed and may contain
> confidential and/or
> >>>>>>>>>> privileged
> >>>>>>>>>> material. Any review, retransmission, dissemination
> >>> or other use
> >>>>>>>>>> of, or
> >>>>>>>>>> taking of any action in reliance upon, this information
> >>>>>> by persons or
> >>>>>>>>>> entities other than the intended recipients is
> prohibited by
> >>>>>>>>>> AgResearch
> >>>>>>>>>> Limited. If you have received this message in error,
> >>>>>> please notify
> >>>>>>>>>> the
> >>>>>>>>>> sender immediately.
> >>>>>>>>>> =
> >>>>>>>>>> =
> >>>>>>>>>>
> >>>>>>
> >>>
> =====================================================================
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Bioperl-l mailing list
> >>>>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> Jason Stajich
> >>>>>>>>> jason at bioperl.org
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> Bioperl-l mailing list
> >>>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>> --------------------------------------------------------------
> >>>>>> ----------------
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> No virus found in this incoming message.
> >>>>>>> Checked by AVG - www.avg.com
> >>>>>>> Version: 8.5.375 / Virus Database: 270.13.5/2219 - Release
> >>>>>> Date: 07/05/09
> >>>>>>> 05:53:00
> >>>>>>
> >>>>>>
> >>>>>> --------------------------------------------------------------
> >>>>>> ------------------
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> No virus found in this incoming message.
> >>>>>> Checked by AVG - www.avg.com
> >>>>>> Version: 8.5.375 / Virus Database: 270.13.5/2220 - Release
> >>>>>> Date: 07/05/09
> >>>>>> 17:54:00
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>
> >>>
> >>> --------------------------------------------------------------
> >>> ------------------
> >>>
> >>>
> >>>
> >>> No virus found in this incoming message.
> >>> Checked by AVG - www.avg.com
> >>> Version: 8.5.375 / Virus Database: 270.13.8/2227 - Release
> >>> Date: 07/09/09
> >>> 05:55:00
> >>>
> >>>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> --------------------------------------------------------------
> ------------------
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 8.5.375 / Virus Database: 270.13.9/2229 - Release
> Date: 07/10/09
> 07:05:00
>
>
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