SOBAcl

SOBAcl is a command line tool for analyzing GFF3 annotations. GFF3 is a standard file format for genomic annotation data. SOBAcl gathers statistics from GFF3 files and can generate a wide variety of tables and graphs.

SOBAcl is intended is a tool for those dealing with genomic sequence annotation who want to view genome wide summaries of their annotation files. For example: SOBAcl would be a useful tool at an annotation jamboree for a newly sequenced organism and when preparing the resulting genome paper; SOBAcl would help those developing annotation tools to quickly evaluate updates to their tool; SOBAcl assists comparative genomics analyses by providing a high-level overview of the genome of multiple organisms. SOBAcl complements genome browsers by providing a summary of all the features annotated in the genome.

SOBAcl is built with Perl and uses Template Tooklit (TT) to generate html/txt reports, the Graphviz library for the ontology graphs, and the GD library for charts.

Documentation

A detailed usage statement for SOBAcl can be viewed by passing the --help parameter to SOBAcl.

SOBAcl --help

A README and INSTALL document are also included with SOBAcl.

Requirements

SOBAcl requires:

• Perl
• The Graphviz library
• The libgd (GD) graphics library
• GraphViz
• Template
• DBI
• Statistics::Descriptive
• Set::IntSpan::Fast
• Text::Table
• Number::Format
• SQL::Abstract
• GO::Parser
• GD::Graph

Download

SOBAcl is available (via Subversion) from:

svn co svn://topaz.genetics.utah.edu/SOBA/trunk SOBA

Mailing List

SOBAcl is supported by the Sequence Ontology Developers Mailing list at:

https://lists.sourceforge.net/lists/listinfo/song-devel