Genome Annotation Library (Version 0.2.2)

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Genome Annotation Library (Version 0.2.2)

Scott Cain
Message forwarded from the Sequence Ontology list; this looks like an excellent tool for anybody who works with GFF3.


---------- Forwarded message ----------
From: Barry Moore <[hidden email]>
Date: Wed, Jan 29, 2014 at 7:58 PM
Subject: [maker-devel] Genome Annotation Library (Version 0.2.2)
To: SO developers <[hidden email]>, [hidden email], "[hidden email] List" <[hidden email]>

The Sequence Ontology is please to announce the release of the Genome Annotation Library (GAL) Version 0.2.2.  GAL is a library of Perl modules that makes working with sequence features in GFF3/GVF files straight forward and intuitive.  GAL also provides numerous parser classes for converting other formats to GFF3 and makes writing new parsers easy. GAL takes advantage of the ontology based relationships captured in SO-based sequence feature data to allow users to easily traverse the relationships between features in a GFF3 file.  In addition to the GAL programming library many scripts utilizing the library are included as well as several stand-alone scripts for working with GFF/GVF and other genomic dataset.

Updates in this version include:

-Adding bin/footprint script
-Adding gal_indexer script
-Adding bin/gene_CDS_footprint script
-New CPAN style html docs for GAL
-Updates to gtf2gff3
-Adding warnings when can not return CDS or protein sequence
-Added progress counter to Storage::SQLite::load_files
-Adding --template option to gff_tool
-Adding templates/
-Adding gal_remove_transcripts and gal_gff_tool
-Adding fix_gvf function to bin/gff_tool
-Added --clean to gal_protein_genes
-Adding GAL::Base::open_file

For more information, to access the GAL docs and to download GAL code please visit:

Barry Moore
Research Scientist
Dept. of Human Genetics
Dept. of Biomedical Informatics
University of Utah
Salt Lake City, UT 84112
<a href="tel:%28801%29%20585-3543" value="+18015853543" target="_blank">(801) 585-3543

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (                     216-392-3087
Ontario Institute for Cancer Research

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