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-   -   Bug#680177: ITP: libnhgri-blastall-perl -- Perl extension for running and parsing NCBI's BLAST 2.x (http://www.linux-archive.org/debian-development/680021-bug-680177-itp-libnhgri-blastall-perl-perl-extension-running-parsing-ncbis-blast-2-x.html)

07-04-2012 09:54 AM

Bug#680177: ITP: libnhgri-blastall-perl -- Perl extension for running and parsing NCBI's BLAST 2.x
 
Package: wnpp
Severity: wishlist
Owner: jenzo@cbv.net


* Package name : libnhgri-blastall-perl
Version : 0.66
Upstream Author : Joseph Ryan <jfryan@nhgri.nih.gov>
* URL : http://genomes.nhgri.nih.gov/
* License : GPL
Programming Lang: Perl
Description : Perl extension for running and parsing NCBI's BLAST 2.x

If you have NCBI's BLAST2 or WU-BLAST installed locally and your environment is already set up you can use Perl's object-oriented capabilities to run your BLAST requests. Also if you have a blastcl3 binary from the toolkit (or binaries from our FTP site) you can run BLAST over the network. There are also some methods to BLAST single sequences against each other using the bl2seq binaries (also in the toolkit and binaries). You can BLAST one sequence against a library of sequences using the blast_one_to_many method. You can format databases with formatdb method. You can also have NCBI::Blastall read existing BLAST reports. If you have a database of repetitive DNA or other DNA you would like to mask out, you can use the mask method to mask the data against these databases. You can either use the filter or result methods to parse the report and access the various elements of the data.



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