[Bioperl-l] cdd-search with remoteblast?
Chris Fields
cjfields1 at gmail.com
Thu Jul 9 15:19:15 EDT 2009
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/RemoteBlast.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
>>>>>> =
>>>>>> =
>>>>>>
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>>>>>
>>>>> --
>>>>> 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
>>>
>>>
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