FEAST: Fast Empirical Algorithms Suggesting Transcripts

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

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)
Genome Organization
Glusman & Smit 2009 (In: Encyclopedia of Complexity and Systems Science. Meyers, Robert, Ed. Volume 4 of 11, pp. 4160-4178. Springer, New York.)
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)

Species-specific parameters and predictions

Species	Freeze	ROAST	Greens	PASTA	CHOWDER	SPLAT	FEAST
human	hg19	params, values	params, values	params, values	params, values	params, values	values, predictions, track
human	hg18	params, values	params, values	params, values	params, values	params, values	values, predictions, track
chimp	panTro2	params, values	params, values	params, values	params, values	params, values	values, predictions, track
orang	ponAbe2	params, values	params, values	params, values	params, values	params, values	values, predictions, track
mouse	mm9	params, values	params, values	params, values	params, values	params, values	values, predictions, track
rat	rn4	params, values	params, values	params, values	params, values	params, values	values, predictions, track
cow	bosTau4	params, values	params, values	params, values	params, values	params, values	values, predictions, track
horse	equCab2	params, values	params, values	params, values	params, values	params, values	values, predictions, track
opossum	monDom5	params, values	params, values	params, values	params, values	params, values	values, predictions, track
platypus	ornAna1	params, values	params, values	params, values	params, values	params, values	values, predictions, track
chicken	galGal3	params, values	params, values	params, values	params, values	params, values	values, predictions, track
zebra-finch	taeGut1	params, values	params, values	params, values	params, values	params, values	values, predictions, track
Chlamidomonas	Chlre4	params, values	params, values	params, values	params, values	params, values	values, predictions, track
Arabidopsis	TAIR10	params, values	params, values	params, values	params, values	params, values	values, predictions, track

To use the custom FEAST track for the UCSC browser: Create a bookmark in your browser, pointing at one of the "track" links in the table above. 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.
Here are some additional, old versions of the FEAST track:

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

Software

Artificial sequence generator, v.2
Tools for computing sequence complexity, v.1
RNAseq-Pi package for processing RNAseq data, v.1
GESTALT Framework, 120126 freeze
GESTALT Genome Browser
GESTALT Workbench

Contact information

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