[Bioperl-l] Problem or Bug with Bio::

[Jason Stajich]

FASTA format has different meanings
AlignIO fasta means Multiple sequence alignment FASTA like this
>seq1
AGATAG-GATGA
>seq2
AGATAGTGA-GA

If you want to parse FASTA (pairwise) search output use
Bio::SearchIO


On Fri, 14 Nov 2003 hyupaik at indiana.edu wrote:

>
>
> #! /local/bin/perl -w
>
> use strict;
> use lib '/home/hy1001/bin';
>
> use Bio::SimpleAlign;
> use Bio::AlignIO;
>
>
> my $in = Bio::AlignIO->new('-file' => 'fastaResult',
>                          '-format' => 'fasta');
> my $aln = $in->next_aln();
>
> my $out = new Bio::AlignIO('-file' => '>testout.fasta',
>                          '-format' => 'fasta');
> $out->write_aln($aln);
>
>
>
>
>
>
> >>crab_chick/1-462
> initninitoptZ-score.bits.E.Smith-Watermanscore.identity.unga
> ppedinaaoverlap--crabaMDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELL
> PASPSLSPFLMRSPIFRMPSWL....crabcMDITIHNPLVRRPLFSWLTPSRIFDQIFG
> EHLQESELLPTSPSLSPFLMRSPFFRMPSWLcrabaETGLSEMRLEKDKFSVNLDVKHFS
> PEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNRK..crabcETGLSEMRLEKDKFSVN
> LDVKHFSPEELKVKVLGDMIEIHGKHEERQDEHGFIAREFSRKcrabaYRIPADVDPLTI
> TSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK.crabcYRIPADVDPLTI
> TSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGSQRK
> >>crab_bovin/1-628
> initninitoptZ-score.bits.E.Smith-Watermanscore.identity.unga
> ppedinaaoverlap--crabaMDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELL
> PASPSLSPFLMRSPIF-RMPSW..........crabbMDIAIHHPWIRRPFFPFHSPSRL
> FDQFFGEHLLESDLFPASTSLSPFYLRPPSFLRAPSWcrabaLETGLSEMRLEKDKFSVN
> LDVKHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNR........crabbIDTGL
> SEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRcraba
> KYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK.....
> ....crabbKYRIPADVDPLAITSSLSSDGVLTVNGPRKQASGPERTIPITREEKPAVT
> AAPKKresiduesinquerysequencesresiduesinlibrarysequencesScomp
> libtstartFriNovdoneFriNovTotalScantime.TotalDisplaytime.Func
> tionusedwasFASTAversion.tNov
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu