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Bio-BioStudio-1.05
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/ Bio::BioStudio::BLAST

NAME

Bio::BioStudio::BLAST

VERSION

Version 1.05

DESCRIPTION

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

FUNCTIONS

make_blast_factory

Returns a Bio::Tools::Run::StandAloneBlastPlus object that can be used to run BLAST queries.

_make_FASTA

creates a FASTA file for BLAST database creation.

Arguments: a hashref of chromosome, where the key is the name and the value is 
              the path, see L<Bio::BioStudio::Basic::gather_versions>
           the BioStudio configuration hashref
           a label

make_BLAST_db

creates a BLAST database.

Arguments: a hashref of chromosomes where the key is the name and the value is
              the path, see L<Bio::BioStudio::Basic::gather_versions>
           the BioStudio configuration hashref
           a label

make_megaBLAST_index

creates a megaBLAST index to speed BLASTing

Arguments: the name of a BLAST database
           the BioStudio configuration hashref
           a label

bl2seq_blastn

Runs a bl2seq on the nucleotide sequences of two features.

Arguments: two L<Bio::DB::SeqFeature> objects
           a L<Bio::Tools::Run::StandAloneBlastPlus> object, probably from 
              the make_blast_factory function

bl2seq_blastp

Runs a bl2seq on the translated sequences of two features.

Arguments: two L<Bio::DB::SeqFeature> objects
           a GeneDesign codon table hashref, from define_codon_table()
           a L<Bio::Tools::Run::StandAloneBlastPlus> object, probably from 
              the make_blast_factory function

COPYRIGHT AND LICENSE

Copyright (c) 2011, BioStudio developers All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

* Neither the name of the Johns Hopkins nor the names of the developers may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.