/ 
bioperl-0.7.0
/ Bio::Tools::BPbl2seq

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     :