homology based gene prediction

Mondow · 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

Mondow · 01-08-2013, 04:34 AM

no reply from anyone?

MeganS · 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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01-07-2013, 11:27 AM	#1
Mondow Junior Member Location: Earth Join Date: Dec 2012 Posts: 4	homology based gene prediction 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

01-08-2013, 04:34 AM	#2
Mondow Junior Member Location: Earth Join Date: Dec 2012 Posts: 4	no reply from anyone?

01-08-2013, 10:38 AM	#3
MeganS Member Location: US Join Date: Sep 2010 Posts: 14	There are a number of annotation pipelines available. MAKER would probably be a good place to start (http://gmod.org/wiki/MAKER)