FEAST: Fast Empirical Algorithms Suggesting Transcripts

An integration of four algorithms: ROAST, Greens, PASTA and CHOWDER.

Publications

A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions
Glusman et al. 2006 (PMID 16543943, PLoS Comp. Biol., supplementary information).
Mining "junk" DNA to find hidden transcriptional gems
Glusman 2009 (GENSIPS 2009, doi 10.1109/GENSIPS.2009.5174348)
Enhancing gene detection with computer generated intergenic regions
Caballero & Glusman 2009 (GENSIPS 2009, doi 10.1109/GENSIPS.2009.5174347)

Code releases

Intergenic sequence generator, v.1
GESTALT Framework, v.1

Parameters

FEAST parameters for hg18, mm9, rn4 and galGal3.

Predictions

Genome-wide FEAST predictions for hg18, mm9, rn4 and galGal3.
Stencil gene analysis for annotated transcripts of hg18.

A custom FEAST track for the UCSC browser

Create a bookmark in your browser, pointing at one of the track links below. Then, when viewing any region in the human genome via the UCSC genome browser, select that bookmark to add the FEAST predictions to your display. You'll typically need to do this just once per session.

Track for hg16 (July 03 freeze)
Track for hg18 (March 06 freeze)

Contact information

Please contact Gustavo Glusman with any queries, comments or suggestions.