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AlignAid 0.0.2

  Date Added: July 27, 2010  |  Visits: 423

AlignAid

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AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20 -nonnegok ); # run the job on the current host my $return_value = $job->submit(outfile => my_results.out); # create an AlignAid cross_match object # specify the alignment program and the queue to override the defaults my $job2 = AlignAid->new( program => cross_match, db => my_db.fa, dir => $dir, fasta => my_query_seqs.fa, queue => LSF); # submit the cross_match jobs to an LSF queue (of compute nodes) my $return_value2 = $job2->submit(outfile => my_output); # kill the queued jobs my $return_value3 = $job2->kill_all; AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the queries into multiple queue jobs. Likewise, if you want to run the alignments locally on a single host, a single change is all that is necessary -- AlignAid will take care of how to invoke the alignment programs and manage the output. AlignAid also has rudimentary support for LSF queue job control; it is possible to kill jobs through AlignAids interface. Whats New in This Release: - Perl.

Requirements: No special requirements
Platforms: Linux
Keyword: Alignaid Alignments Libraries Locally Lsf Module Perl Perl Module Programming Queue Sequence Sequence Alignments
Users rating: 0/10

License: Freeware Size: 348.16 KB
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