NAME

Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.

SYNOPSIS

  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;

DESCRIPTION

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.)

FEEDBACK

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/

AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu

ACKNOWLEDGEMENTS

Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port)

COPYRIGHT

BPlite.pm is copyright (C) 1999 by Ian Korf.

DISCLAIMER

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     :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq