Difference between revisions of "SOBA"
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{{ComponentBox|{{SobaResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{GMODAmericas2011BoxItem|2011 GMOD Spring Training|GMOD Spring Training|March 8-12}}| | |}} | {{ComponentBox|{{SobaResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{GMODAmericas2011BoxItem|2011 GMOD Spring Training|GMOD Spring Training|March 8-12}}| | |}} | ||
| − | '''[http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA]''' is a web interface tool for analyzing [[GFF3]] annotations. [[GFF3]] is a standard file format for genomic annotation data. SOBA gathers statistics from GFF3 and | + | '''[http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA]''' is a command line (SOBAcl) and web interface tool 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. |
| − | * Summary | + | |
| + | The web version of SOBA will produce the following: | ||
| + | * Summary statistics of feature types and attributes used | ||
* Histograms of feature lengths | * Histograms of feature lengths | ||
* Graphs of [http://www.sequenceontology.org Sequence Ontology] terms used | * Graphs of [http://www.sequenceontology.org Sequence Ontology] terms used | ||
| Line 14: | Line 16: | ||
* Suggestions to improve SO compliance for invalid terms | * Suggestions to improve SO compliance for invalid terms | ||
| − | SOBA is intended to be a tool for people who are dealing with genomic sequence annotation, and want a summary of the contents of their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism, where the annotations are being created; SOBA would help those developing annotation tools quickly evaluate updates to their tool; SOBA | + | In addition, the command line version produces a wide variety of table, figures and graphs of the data in a [[GFF3] file as well as the ability to filter the content, and produce complex custom reports. |
| + | |||
| + | SOBA is intended to be a tool for people who are dealing with genomic sequence annotation, and want a summary of the contents of their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism, where the annotations are being created; 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 in that it provides a summary of all the features annotated in the genome. | ||
| + | |||
| + | SOBA is built with Perl (and JavaScript for the web interface). The web interface uses {{CPAN|CGI::Application}} as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and {{GlossaryLink|AJAX|AJAX}}. Both versions of SOBA use the [http://template-toolkit.org/ Template Tooklit (TT)] to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who's willing to learn the fairly simple template language of TT (you don't need to know Perl or any other programming to use TT). | ||
| + | |||
| + | = Documentation = | ||
| + | |||
| + | Documentation for the web interface to SOBA is available on the [http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis 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: | ||
| + | |||
| + | <pre> | ||
| + | SOBAcl --help | ||
| + | </pre> | ||
| + | |||
| + | A README and INSTALL document included with SOBAcl as well. | ||
| + | |||
| + | = Requirements = | ||
| + | |||
| + | The web interface to SOBA should work on any modern browser that has Javascript enabled. | ||
| + | |||
| + | SOBAcl requires: | ||
| + | |||
| + | Perl | ||
| + | graphviz | ||
| + | libgd | ||
| + | [www.cpan.org GraphViz] | ||
| + | [www.cpan.org Template] | ||
| + | [www.cpan.org Getopt::Long] | ||
| + | [www.cpan.org DBI] | ||
| + | [www.cpan.org Template] | ||
| + | [www.cpan.org Statistics::Descriptive] | ||
| + | [www.cpan.org Set::IntSpan::Fast] | ||
| + | [www.cpan.org Text::Table] | ||
| + | [www.cpan.org Number::Format] | ||
| + | [www.cpan.org SQL::Abstract] | ||
| + | [www.cpan.org GO::Parser] | ||
| − | |||
= Download = | = Download = | ||
| + | |||
| + | The SOBA web interface is available at: | ||
| + | |||
| + | http://www.sequenceontology.org/cgi-bin/soba.cgi | ||
| + | |||
| + | SOBAcl is available (via svn) from: | ||
| + | |||
| + | svn co svn://malachite.genetics.utah.edu/SOBA/trunk SOBA | ||
= Mailing List(s) = | = Mailing List(s) = | ||
| + | |||
| + | SOBA is supported by the Sequence Ontology Developers Mailing list at: | ||
| + | |||
| + | https://lists.sourceforge.net/lists/listinfo/song-devel | ||
= See Also = | = See Also = | ||
* [http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA page] at [http://www.sequenceontology.org SequenceOntology.org] | * [http://www.sequenceontology.org/wiki/index.php/SOBA_-_Sequence_Ontology_Bioinformatics_Analysis SOBA page] at [http://www.sequenceontology.org SequenceOntology.org] | ||
Revision as of 01:13, 7 March 2011
__NOTITLE__
This page or section is under construction.
SOBA is a GFF3 analysis tool that has been nominated and approved for GMOD Membership. It is in the process of being incorporated into GMOD.
SOBA is a command line (SOBAcl) and web interface tool 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 version produces a wide variety of table, figures and graphs of the data in a [[GFF3] file as well as the ability to filter the content, and produce complex custom reports.
SOBA is intended to be a tool for people who are dealing with genomic sequence annotation, and want a summary of the contents of their annotation files. For example: SOBA would be a useful tool at an annotation jamboree for a newly sequenced organism, where the annotations are being created; 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 in that it provides a summary of all the features annotated in the genome.
SOBA is built with Perl (and JavaScript for the web interface). The web interface uses CGI::Application as a Perl webapp framework and the JQuery JavaScript library for Web 2.0 effects and AJAX. Both versions of SOBA use the Template Tooklit (TT) to generate html/txt reports, graphviz for the ontology graphs, and GD for charts. Template Toolkit makes extensibility very easy, at least for someone who's willing to learn the fairly simple template language of TT (you don't need to know Perl or any other programming to use TT).
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 included with SOBAcl as well.
Requirements
The web interface to SOBA should work on any modern browser that has Javascript enabled.
SOBAcl requires:
Perl graphviz libgd [www.cpan.org GraphViz] [www.cpan.org Template] [www.cpan.org Getopt::Long] [www.cpan.org DBI] [www.cpan.org Template] [www.cpan.org Statistics::Descriptive] [www.cpan.org Set::IntSpan::Fast] [www.cpan.org Text::Table] [www.cpan.org Number::Format] [www.cpan.org SQL::Abstract] [www.cpan.org GO::Parser]
Download
The SOBA web interface is available at:
http://www.sequenceontology.org/cgi-bin/soba.cgi
SOBAcl is available (via svn) from:
svn co svn://malachite.genetics.utah.edu/SOBA/trunk SOBA
Mailing List(s)
SOBA is supported by the Sequence Ontology Developers Mailing list at:
https://lists.sourceforge.net/lists/listinfo/song-devel
