Réf. : Re: [Bioperl-l] problem with pir sequence
sebastien.frade at bayercropscience.com
sebastien.frade at bayercropscience.com
Tue Jan 27 09:55:36 EST 2004
Here is the pir file I use.
>P1;S14946
2S seed storage protein large chain - Brazil nut
N;Alternate names: albumin 2S precursor
C;Species: Bertholletia excelsa (Brazil nut)
C;Date: 21-Nov-1993 #sequence_revision 26-May-1995 #text_change 21-Jul-2000
C;Accession: S14946; S14479; S06252; S21640; B25802
R;Gander, E.S.; Holmstroem, K.O.; de Paiva, G.R.; de Castro, L.A.B.; Carneiro,
M.; Grossi de Sa, M.F.
Plant Mol. Biol. 16, 437-448, 1991
A;Title: Isolation, characterization and expression of a gene coding for a 2S
albumin from Bertholletia excelsa (Brazil nut).
A;Reference number: S14946; MUID:91370890; PMID:1840683
A;Accession: S14946
A;Status: preliminary
A;Molecule type: DNA
A;Residues: 1-146 <GAN>
A;Cross-references: EMBL:X54490; NID:g17710; PIDN:CAA38362.1; PID:g17711
A;Note: the authors translated the codon CTT for residue 13 as Val and GTC for
residue 14 as Leu
R;Bassuener, R.; Schlesier, B.
submitted to the EMBL Data Library, December 1990
A;Reference number: S14479
A;Accession: S14479
A;Status: preliminary
A;Molecule type: DNA
A;Residues: 1-146 <BAS>
A;Cross-references: EMBL:X57027; NID:g17714; PID:g17715
R;Altenbach, S.B.; Pearson, K.W.; Leung, F.W.; Sun, S.S.M.
Plant Mol. Biol. 8, 239-250, 1987
A;Title: Cloning and sequence analysis of a cDNA encoding a Brazil nut protein
exceptionally rich in methionine.
A;Reference number: S06252
A;Accession: S06252
A;Status: not compared with conceptual translation
A;Molecule type: mRNA
A;Residues: 1-146 <ALT>
A;Experimental source: clone pHS-3
A;Note: part of this sequence, including the amino end of the large chain, was
confirmed by protein sequencing
R;Bassuener, R.; Schlesier, B.
submitted to the EMBL Data Library, December 1990
A;Reference number: S21640
A;Accession: S21640
A;Status: preliminary
A;Molecule type: DNA
A;Residues: 1-146 <BA2>
A;Cross-references: EMBL:X57028; NID:g17716; PID:g17717
R;Ampe, C.; Van Damme, J.; de Castro, L.A.B.; Sampaio, M.J.A.M.; Van Montagu,
M.; Vandekerckhove, J.
Eur. J. Biochem. 159, 597-604, 1986
A;Title: The amino-acid sequence of the 2S sulphur-rich proteins from seeds of
Brazil nut (Bertholletia excelsa H.B.K.).
A;Reference number: A91173; MUID:87004679; PMID:3758080
A;Accession: B25802
A;Molecule type: protein
A;Residues: 70-90,'E',92-121,'M',123-125,'L',127-142 <AMP>
C;Genetics:
A;Introns: 60/3
C;Superfamily: wheat alpha-amylase inhibitor
F;1-22/Domain: signal sequence #status predicted <SIG>
F;23-46/Domain: propeptide #status predicted <PRO>
F;47-69/Product: seed storage protein small chain #status predicted <SCH>
F;70-146/Product: seed storage protein large chain #status experimental <LCH>
MAKISVAAAALLVLMALGHATAFRATVTTTVVEEENQEECREQMQRQQMLSHCRMYMRQQ
MEESPYQTMPRRGMEPHMSECCEQLEGMDESCRCEGLRMMMMRMQQEEMQPRGEQMRRMM
RLAENIPSRCNLSPMRCPMGGSIAGF*
Sébastien Frade
BioInformatic Team
BAYER CropScience / BioScience
4 rue Pierre FONTAINE
91058 EVRY – France
tel: 33 (0) 1 69 47 61 52
fax: 33 (0) 1 69 47 61 42
mail:
sebastien.frade at bayercropscience.com
http://bioinfo.evry.fr.bayercropscience
Pour : sebastien.frade at bayercropscience.com
cc : bioperl-l at bioperl.org
Objet : Re: [Bioperl-l] problem with pir sequence
bioperl-l-bounces at portal.open-bio.
org
27/01/2004 15:51
pir support is pretty minimal - you'll have to send a copy of the original
seq file for someone to see if they can help.
On Tue, 27 Jan 2004 sebastien.frade at bayercropscience.com wrote:
>
>
>
>
> Hi,
>
> I'ma working with pir files, and i have a problem during reading file with
> bioperl.
>
> here is the code,
>
>
>
> use strict;
>
> use Bio::SeqIO;
>
> my $filename="deux.S64";
>
> print new Bio::Tools::GuessSeqFormat( -file => $filename )->guess,"\n";
>
>
> my $in = Bio::SeqIO->new(-file => $filename , '-format' => 'pir');
> my $seq;
>
> while ($seq = $in->next_seq() ) {
> print "Sequence ",$seq->id," first 10 bases ",$seq->subseq(1,10),"\n";
> }
>
>
> and here is the error message
>
> -------------------- WARNING ---------------------
> MSG: seq doesn't validate, mismatch is 1
> ---------------------------------------------------
>
> ------------- EXCEPTION -------------
> MSG: Attempting to set the sequence to
>
[N;Alternatenames:albumin2SprecursorC;Species:BertholletiaexcelsaBrazilnutC;Date:21-Nov-1993#sequence_revision26-May-1995#text_change21-Jul-2000C;Accession:S14946;S14479;S06252;S21640;B25802R;GanderES;HolmstroemKO;dePaivaGR;deCastroLAB;CarneiroM;GrossideSaMFPlantMolBiol16437-4481991A;Title:Isolationcharacterizationandexpressionofagenecodingfora2SalbuminfromBertholletiaexcelsaBrazilnutA;Referencenumber:S14946;MUID:91370890;PMID:1840683A;Accession:S14946A;Status:preliminaryA;Moleculetype:DNAA;Residues:1-146<GAN]
> which does not look healthy
> STACK Bio::PrimarySeq::seq /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/PrimarySeq.pm:268
> STACK Bio::PrimarySeq::new /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/PrimarySeq.pm:217
> STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.8.0/Bio/Seq.pm:498
> STACK Bio::Seq::SeqFactory::create /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/Seq/SeqFactory.pm:126
> STACK Bio::SeqIO::pir::next_seq /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/SeqIO/pir.pm:122
> STACK toplevel pir.pl:15
>
>
> Is there a problem with my code ?
>
> Please help me!!!
>
>
>
>
>
>
>
> Sébastien Frade
> BioInformatic Team
> BAYER CropScience / BioScience
> 4 rue Pierre FONTAINE
> 91058 EVRY – France
>
> tel: 33 (0) 1 69 47 61 52
>
> fax: 33 (0) 1 69 47 61 42
>
> mail:
> sebastien.frade at bayercropscience.com
>
> http://bioinfo.evry.fr.bayercropscience
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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