Map ESTs to re annotated genome to get updated gene annotations

Question

[gtho123]

I work on a plant species with a reasonably large genome which has recently been reannotated with new annotations.

I have an EST library I would like to re label with the newest corresponding gene annotations. The current labels are from an annotation version a couple of versions ago so the translation intructions are no longer on the web.

Is there an easy way to map the ESTs to the genome or genome CDS and then extract the gene annotations to label the ESTs with?

[Giovanni M Dall'Olio]

Many years ago, before exome sequencing, I used exonerate to map EST to a reference genome to identify alternative splicing events. Exonerate may be better than Blast because it has a model to specifically align ESTs to a genome, dealing with very long gaps (introns) and with exon/intron boundaries. In any case, your blast search is probably enough already. The EST technology is a bit old and I am afraid I don't know many recent tools that can handle it, sorry if I can't be more of help :-)

[gtho123]

As a work around I just BLASTed the ESTs to the genome CDS and used a perl script to get the best hits. Then matched the annotation of the best hit to the EST.