Bio-LITE-Taxonomy-NCBI-Gi2taxid

The NCBI site offers a file to map gene and protein sequences (GIs) with their corresponding taxon of origin (Taxids). If you want to use this information inside a Perl script you will find that (given the high amount of sequences available) it is fairly inefficient to store this information in a regular hash. Only for creating such a hash you will need more than 10 GBs of system memory.

This is a very simple module that has been designed to efficiently map NCBI GIs to Taxids with speed as the primary goal. It is designed to be able to process a high number of GIs very fast and with low memory usage. It is even faster than using a SQL database to retrieve the mappings or using a local DBHash.

To achieve this, it uses a binary index that can be created with the function C<new_dict>. This index has to be created one time for each mapping file.

The original mapping files can be downloaded from the NCBI site at the following address: L<ftp://ftp.ncbi.nih.gov/pub/taxonomy/>.

INSTALLATION

To install this module, run the following commands:

	perl Makefile.PL
	make
	make test
	make install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the
perldoc command.

    perldoc Bio::LITE::Taxonomy::NCBI::Gi2taxid

You can also look for information at:

    RT, CPAN's request tracker
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-LITE-Taxonomy-NCBI-Gi2taxid

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/Bio-LITE-Taxonomy-NCBI-Gi2taxid

    CPAN Ratings
        http://cpanratings.perl.org/d/Bio-LITE-Taxonomy-NCBI-Gi2taxid

    Search CPAN
        http://search.cpan.org/dist/Bio-LITE-Taxonomy-NCBI-Gi2taxid/


LICENSE AND COPYRIGHT

Copyright (C) 2010 Miguel Pignatelli

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.

