GMOD
SOBA
Status
- Mature release
- Development: maintenance
- Support: active
Resources
Contents
- 1 About Sequence Ontology Bioinformatics Analysis (SOBA)
- 2 Downloads
- 3 Using SOBA
- 4 Publications, Tutorials, and Presentations
- 5 Contacts and Mailing Lists
- 6 More on SOBA
About Sequence Ontology Bioinformatics Analysis (SOBA)
SOBA, Sequence Ontology Bioinformatics Analysis, is a command line tool and web application for analyzing GFF3 annotations. GFF3 is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 files and renders them as tables and graphs.
The web version of SOBA will produce the following:
- Summary statistics of feature types and attributes used
- Histograms of feature lengths
- Graphs of Sequence Ontology terms used
- Histograms of intron density
- Suggestions to improve SO compliance for invalid terms
In addition, the command line tool (SOBAcl) flexibly produces a much wider variety of tables, figures and graphs based on the data in a GFF3 file as well as the ability to produce complex and extensible custom reports via a robust template system.
SOBA is intended as a tool for those dealing with genomic sequence annotation who want to view genome wide summaries of their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism and when preparing the resulting genome paper; SOBA would help those developing annotation tools to quickly evaluate updates to their tool; SOBA assists comparative genomics analyses by providing a high-level overview of the genome of multiple organisms. SOBA complements genome browsers by providing a summary of all the features annotated in the genome.
Visit the SOBA website.
Downloads
- SOBAcl is available (via Subversion) from:
svn co svn://topaz.genetics.utah.edu/SOBA/trunk SOBA
Using SOBA
System Requirements
SOBA is built with Perl and uses Template Toolkit (TT) to generate html or text reports, GraphViz for ontology graphs, and GD for charts. SOBAweb uses CGI::Application as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and AJAX.
SOBA web
The web interface to SOBA should work on any modern browser that has Javascript enabled.
SOBAcl
SOBAcl requires a number of Perl libraries, as well as the Graphviz and libgd graphics library:
- The Graphviz library
- The libgd graphics library
- Perl
- GraphViz
- Template Toolkit
- DBI
- Statistics::Descriptive
- Set::IntSpan::Fast
- Text::Table
- Number::Format
- SQL::Abstract
- GO::Parser from go-perl
- GD::Graph
Installation
Install documentation is included in the SOBAcl download.
Documentation
Documentation for the web interface to SOBA is available on the Sequence Ontology Wiki as well as via tool-tips on the site itself.
Documentation for the command line version - SOBAcl - is available as a usage statement with the script itself:
SOBAcl --help
A README and INSTALL document are also included with SOBAcl.
Publications, Tutorials, and Presentations
Tutorials
SOBA
Tutorial
taught as part of the 2013 GMOD Summer
School
Contacts and Mailing Lists
SOBA is supported by the Sequence Ontology Developers Mailing list.
More on SOBA
Raw tool data at SOBA/tool data
Facts about “SOBA”
| | | |—-|—-| | Has website | http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis + |