Boulder

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Boulder/Blast.pm  view on Meta::CPAN

The total length of the sequence that was hit

=item Signif

The significance of the hit.  If there are multiple HSPs in the hit,
this will be the most significant (smallest) value.

=item Identity

The percent identity of the hit.  If there are multiple HSPs, this
will be the one with the highest percent identity.

=item Expect

The expectation value for the hit.  If there are multiple HSPs, this
will be the lowest expectation value in the set.

=item Hsps

One or more sub-sub-tags, pointing to a nested record containing
information about each high-scoring segment pair (HSP).  See the next

Boulder/Blast.pm  view on Meta::CPAN

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=head1 EXAMPLE BLASTN RUN

This output was generated by the I<quickblast.pl> program, which is
located in the F<eg/> subdirectory of the I<Boulder> distribution
directory.  It is a typical I<blastn> (nucleotide->nucleotide) run;
however long lines (usually DNA sequences) have been truncated.  Also
note that per the Boulder protocol, the percent sign (%) is escaped in
the usual way.  It will be unescaped when reading the stream
back in.

 Blast_run_date=Fri Nov  6 14:40:41 1998
 Blast_db_date=2:40 PM EST Nov 6, 1998
 Blast_parms={
   Hspmax=10
   Expectation=10
   Matrix=+5,-4
   Ctxfactor=2.00

ChangeLog  view on Meta::CPAN

	
2000-07-13  Lincoln Stein  <lstein@formaggio.cshl.org>
	* (version 1.20)
	* Fixes to Boulder::Genbank provided by Lester Hui.
	  Now  handles repeated multivalued features better.

2000-06-08  Lincoln Stein  <lstein@cshl.org>

	* Fixed Boulder::Blast::NCBI parsing error that caused it to miss some HSPs
	* Fixed Boulder::Blast::{NCBI,WU} treatment of % identity -- had been returning
	  identity as a fraction of 1 rather than a percentage (as documented)

1999-12-02  Lincoln Stein  <lstein@cshl.org>

	* Fixed parameter bug in File accessor for Boulder::Genbank.
	* Documented  problems with flock() across NFS filesystems.
	* Boulder::Genbank no longer "eats" the list of accession numbers
	passed to it.

docs/blast_tags.txt  view on Meta::CPAN

	following subtags:

	Name	The name of the sequence that was hit.

	Length	The total length of the sequence that was hit

	Signif	The significance of the hit.  If there are multiple
		HSPs in the hit, this will be the most significant
		(smallest) value.

	Identity The percent identity of the hit.  If there are
		multiple HSPs, this will be the one with the
		highest percent identity.

	Expect	The expectation value for the hit.  If there are
		multiple HSPs, this will be the lowest expectation
		value in the set.

	Hsps	One or more sub-sub-tags, pointing to a nested record
		containing information about each high-scoring segment
		pair (HSP).  See section (5) below.

5. The Hsp records

docs/blast_tags.txt  view on Meta::CPAN

	These three tags contain strings which, together, create the
	gapped alignment of the query sequence with the subject
	sequence.

EXAMPLES
--------

1. A BLASTN run

Here is the output from a typical blastn (nucleotide->nucleotide)
run.  Long lines have been truncated.  Note also that the percent sign 
(%) is escaped in the usual way.  It will be unescaped when reading
the boulder stream back in.

Blast_run_date=Fri Nov  6 14:40:41 1998
Blast_db_date=2:40 PM EST Nov 6, 1998
Blast_parms={
  Hspmax=10
  Expectation=10
  Matrix=+5,-4
  Ctxfactor=2.00