Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. use Bio::Tools::BPbl2seq; my $report = Bio::Tools::BPbl2seq->new(-file => 't/bl2seq.out'); $report->query; $report->score; $report->bits; $report->percent; $report->P; $report->match; $report->positive; $report->length; $report->querySeq; $report->sbjctSeq; $report->homologySeq; $report->subject->start; $report->subject->end; $report->subject->seqname; BPbl2seq is a package for parsing BLAST bl2seq reports. BLAST bl2seq is a program for comparing and aligning two sequences using BLAST. Although the report format is similar to that of a conventional BLAST, there are a few differences so that the standard bioperl BLAST parsers Blast.pm and BPlite are unable to read bl2seq reports directly. From the user\'s perspective, the main difference between bl2seq and other blast reports is that the bl2seq report does not print out the name of the first of the two aligned sequences. (The second sequence name is given in the report as the name of the "hit"). Consequently, BPbl2seq has no way of identifying the name of the initial sequence unless it is passed to constructor as a second argument as in: my $report = Bio::Tools::BPbl2seq->new(\*FH, "ALEU_HORVU"); If the name of the first sequence is not passed to BPbl2seq.pm in this manner, the name of the first sequence will be left as "unknown". (Note that to preserve a common interface with the other BLAST programs the two sequences being compared are referred to in bl2seq as "query" and "subject" although this is perhaps a bit misleading when simply comparing 2 sequences as opposed to querying a database.)

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email: schattner@alum.mit.edu Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port) BPlite.pm is copyright (C) 1999 by Ian Korf. This software is provided "as is" without warranty of any kind.

new
Title : new Function: Create a new Bio::Tools::BPbl2seq object Returns : Bio::Tools::BPbl2seq Args : -file input file (alternative to -fh) -fh input stream (alternative to -file) -queryname name of query sequence

P
Title : P Usage : $hsp->P(); Function : returns the P (significance) value for a HSP Example : Returns : (double) significance value Args :

percent
Title : percent Usage : $hsp->percent(); Function : returns the percent matching Example : Returns : (double) percent matching Args :

match
Title : match Usage : $hsp->match(); Function : returns the match Example : Returns : (double) frac_identical Args :

positive
Title : positive Usage : $hsp->positive(); Function : returns the number of positive hits Example : Returns : (int) number of positive residue hits Args :

querySeq
Title : querySeq Usage : $hsp->querySeq(); Function : returns the query sequence Example : Returns : (string) the Query Sequence Args :

sbjctSeq
Title : sbjctSeq Usage : $hsp->sbjctSeq(); Function : returns the Sbjct sequence Example : Returns : (string) the Sbjct Sequence Args :

homologySeq
Title : homologySeq Usage : $hsp->homologySeq(); Function : returns the homologous sequence Example : Returns : (string) homologous sequence Args :

qs
Title : qs Usage : $hsp->qs(); Function : returns the Query Sequence (same as querySeq) Example : Returns : (string) query Sequence Args :

ss
Title : ss Usage : $hsp->ss(); Function : returns the subject sequence ( same as sbjctSeq) Example : Returns : (string) Sbjct Sequence Args :

hs
Title : hs Usage : $hsp->hs(); Function : returns the Homologous Sequence (same as homologySeq ) Example : Returns : (string) Homologous Sequence Args : alignment using the BLAST algorithm."