ESTs, ORFs and curated databases

[Stephen Rudd]

Bioinformaticians,

I am wanting to automatically extract ORFs from cDNA sequences. I will
have somewhere in the region of 50,000 cDNAs from various plant
species (sugarbeet, barley, maize). Many of these sequences will be orthologues to known
Arabidopsis genes, and I would like to automatcially extract a long ORF that will stem
from several frames (due to sequencing errors and artefacts) rather
than just the longest ORF, or a collection of long ORFs. Could anyone
kindly point me in the right direction ? Tools such as EMBOSS getseq
often identify the wrong sequences and the cDNA sequences can be ugly !

How has anyone else dealt with this problem, has anyone dealt with it
?

Thanks for your help,

Stephen


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