homology based gene prediction

Mondow

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Join Date: Dec 2012

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homology based gene prediction

01-07-2013, 11:27 AM

Can anyone help me with my project design, im very new in this field..I need to do structural annotation..I have paired end data (illumina) and hv performed assembly which produced ~30000 contigs (multifasta file)

Now from this set of contigs, I will need to perform gene prediction (abinitio and homology search). But im not sure the exact way to do this...for example, how am i going to perform blast search over this 30k contigs, in what form the output data should look like,etc until i get a nice set of predicted gene model. I dont have programing skills which makes it hard but im learning it from scratch.

Help me, thnks
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Mondow

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01-08-2013, 04:34 AM

no reply from anyone?
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MeganS

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01-08-2013, 10:38 AM

There are a number of annotation pipelines available. MAKER would probably be a good place to start (http://gmod.org/wiki/MAKER)
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