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Old 06-11-2011, 09:33 AM   #1
1bioinfo
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Location: Toronto

Join Date: Jun 2011
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Default finding gene from scaffolds, no annotation available

Hello,

I have all scaffolds of a bird genome from Illumina sequencing platform, I blast it against chicken genome to find the genes. Since there are millions of scaffolds it takes too long to find and visualize the genes with Geneious Pro software, The annotation file for chicken is available but not for my bird of interest (we have only scaffolds and contigs).
I appreciate if anyone can help me to find a very fast computational way for finding genes.

Thanks
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Old 06-24-2011, 11:52 PM   #2
jeremyrualosr
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Location: Baltimore, MD

Join Date: Mar 2011
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Default Try Geneious Support and UserForum

The support and development team at Biomatters can help you... post on the Geneious User Forum and email [email protected] with your intended workflow...I'll give it a go and let you know what I come up with...
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Old 06-25-2011, 09:32 AM   #3
DZhang
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Location: East Coast, US

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Default

Hi 1bioinfo,

You may predict genes first in your contigs (http://www.cbcb.umd.edu/research/genefinding.shtml), and then use other tools (blast2go or blastx or iprscan) to annotate them. For a project of your size, it will involve tons of efforts...

Best regards,
Douglas
www.contigexpress.com
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