Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2.

ABSTRACT:

Background

The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and ab initio gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of Chlamydomonas genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve ab initio gene finding in Chlamydomonas, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 Chlamydomonas EST entries in GenBank using the EST assembly tool PASA.

Results

The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2,

SUBMITTER: Kwan AL 

PROVIDER: S-EPMC2694837 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature