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Development of Compendium for Esophageal Squamous Cell Carcinoma

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B2G-FAR, a species-centered GO annotation repository.

Stefan Götz¹, Roland Arnold, Patricia Sebastián-León

¹Bioinformatics and Genomics Department, Centro de Investigaciones Príncipe Felipe (CIPF), Valencia, Spain. sgoetz@cipf.es

Bioinformatics (Oxford, England)

|February 22, 2011

Summary

The Blast2GO Functional Annotation Repository (B2G-FAR) offers functional genomics data for over 2000 species, aiding researchers, especially those studying non-model organisms. This resource provides GO term predictions for millions of protein sequences, enhancing biological data accessibility.

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Area of Science:

Bioinformatics
Functional Genomics
Computational Biology

Background:

High-throughput technologies and computational tools like Gene Ontology (GO) have advanced functional genomics.
Biologists, particularly those working with non-model organisms, face challenges with limited or unavailable functional annotation data.
Retrieving, summarizing, and querying functional genomics data can be difficult for researchers.

Purpose of the Study:

To develop a bioinformatics resource, the Blast2GO Functional Annotation Repository (B2G-FAR), for providing functional information on uncharacterized sequences.
To offer data mining tools for analyzing a wider range of species than currently available.
To support functional genomics research, especially for non-model organisms, by improving access to functional annotation.

Main Methods:

Applied the Blast2GO functional annotation engine in a high-throughput manner to all publicly available sequences.
Utilized BLAST search alignments from the SIMAP database for GO term predictions.
Generated GO annotations for approximately 150,000 different taxa, focusing on 2000 species with the highest coverage.

Main Results:

Created B2G-FAR, a repository with GO term predictions for over 13.2 million non-redundant protein sequences.
Made functional annotations available for 2000 species, with a focus on high coverage.
Included functional annotations for 17 non-model organism Affymetrix GeneChips in a dedicated section.

Conclusions:

B2G-FAR offers accessible and exhaustive functional annotation for 2000 species.
The resource balances annotation quality and quantity, significantly supporting functional genomics research.
B2G-FAR is particularly beneficial for researchers working with non-model organisms due to improved data accessibility.