Augustus [Chlamydomonas]

Predictions for Chlamydomonas reinhardtii (assembly 4):

AUGUSTUS was trained in collaboration with Erik F.Y. Hom (Harvard) and Chun Liang (Miami University, Ohio) on Chlamydomonas reinhardtii.

These predictions are based on the JGI-Assembly v4. We thank the Joint Genome Institute/Stanford Human Genome Center for giving us access to version 4 of the Chlamydomonas genome.

The predictions incorporate publicly available EST sets and also ESTs that have been cleaned as in Liang, C., Liu, Y., Liu, L., Davis, A.C., Shen, Y. and Q.Q. Li (2008). The gene structures and EST alignments are displayed on this Chlamydomonas genome browser. For more info on the ESTs go to Chun Liang's chlamy EST-Terminus site.

The u9 predictions are displayed at the phytozome chlamy browser.

If you download and use these predictions for your work, please kindly let us know so we don't end up duplicating similar analysis efforts (and we can keep you informed as updates become available). You may acknowledge our work by citing this website.

Extrinsic parameters for hint integration:

The extrinsic parameter file extrinsic.Specht.paper.cfg was used in the manuscript "Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome" by Specht et al.

Download whole gene set:

version 9:
augustus.u9.gtf.gz (may have to do a "grep -v" to remove lines you don't need),
augustus.u9.aa.gz (protein sequences)
augustus.u9.gff.gz (with some info about evidence support)

version 5 (only for reference, avoid using this):
augustus.u5.aa, augustus.u5.aa.gz
augustus.u5.gbrowse, augustus.u5.gbrowse.gz

Functional annotation and mappings to other gene sets have been compiled by Erik.

or retrieve selected protein sequences:

AUGUSTUS chlamy transcript names (e.g. "Au9.Cre13.g574100.t1, Au9.Cre13.g574050.t1, chromosome10;u5g5.t1")

BLAST server to BLAST sequences against this AUGUSTUS protein set of Chlamy. Has links to the Genome Browser.
Sorted list of transcripts. This is sorted by amount of supporting evidence and has links to the Browser. (Warning: large table)

Mario Stanke,11/6/08