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Bio-BioStudio-1.03
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/ Bio::BioStudio::BLAST

NAME

BioStudio::BLAST

VERSION

Version 1.03

DESCRIPTION

BioStudio functions for BLAST functionality

FUNCTIONS

_make_FASTA() given a hashref of chromosomes (where the key is the name and the value is the path, see Bio::BioStudio::Basic::gather_versions()), the BioStudio config hashref, and a label, creates a FASTA file that contains all of their sequences for BLAST database creation

make_BLAST_db() given a hashref of chromosomes (where the key is the name and the value is the path, see Bio::BioStudio::Basic::gather_versions()), the BioStudio config hashref, and a label, creates a BLAST database containing all of the chromosome sequences in the hashref

make_megaBLAST_index() given the name of a BLAST database, a BioStudio config hashref, and a label, creates a megaBLAST index to speed BLASTing

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

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.