NAME

Bio::MLST::Blast::BlastN - Wrapper around NCBI BlastN

VERSION

version 1.133090

SYNOPSIS

Wrapper around NCBI BlastN. Run NCBI blast and find the top hit.

use Bio::MLST::Blast::BlastN;

my $blast_database= Bio::MLST::Blast::BlastN->new(
  blast_database => 'output_contigs',
  query_file     => 'alleles/adk.tfa',
  word_size      => 500,
  exec           => 'blastn'
);
$blast_database->top_hit();

METHODS

top_hit

Returns a hash containing details about the top blast result.

The attributes returned in the hash are: allele_name percentage_identity source_name source_start source_end reverse contamination

SEE ALSO

• Bio::MLST::Blast::Database

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007