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Old 04-30-2012, 11:29 AM   #1
tomybou
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Location: france

Join Date: Jan 2012
Posts: 2
Default Help internship prediction proteins

Hi everyone,
I'm doing an internship in bioinformatics and I am a little lost... I hope I can find some help here.
I have to predict the proteins of a little known species of plant, by similarity with the already known proteins of a close species.
I have the result file of a 454 pyrosequencing of the "species to study" transcriptome (56 000 contigs), and the fasta file of the "already known close proteins" (53 000 proteins).
Following the advices of my boss I have used the alignement tool Exonerate (model protein2genome) to find similarities between the contigs and the proteins known.
It took 6 days to accomplish.
But Exonerate seems to align only parts of which seems to be the protein (even when I lower the score), forgetting the ends and beginings, so it would be very difficult to write a program predicting the exact proteins.
Do you have advices or an idea of which alignement tool should I use (localy)?
Thank you very much,
Tom
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