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1bioinfo 06-11-2011 09:33 AM

finding gene from scaffolds, no annotation available

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.


jeremyrualosr 06-24-2011 11:52 PM

Try Geneious Support and UserForum
The support and development team at Biomatters can help you... post on the Geneious User Forum and email with your intended workflow...I'll give it a go and let you know what I come up with...

DZhang 06-25-2011 09:32 AM

Hi 1bioinfo,

You may predict genes first in your contigs (, 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,

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