finding gene from scaffolds, no annotation available

1bioinfo · 06-11-2011, 08:33 AM

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

jeremyrualosr · 06-24-2011, 10:52 PM

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

DZhang · 06-25-2011, 08:32 AM

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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06-11-2011, 08:33 AM	#1
1bioinfo Junior Member Location: Toronto Join Date: Jun 2011 Posts: 1	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

06-24-2011, 10:52 PM	#2
jeremyrualosr Junior Member Location: Baltimore, MD Join Date: Mar 2011 Posts: 3	Try Geneious Support and UserForum The support and development team at Biomatters can help you... post on the Geneious User Forum and email support@biomatters.com with your intended workflow...I'll give it a go and let you know what I come up with...

06-25-2011, 08:32 AM	#3
DZhang Senior Member Location: East Coast, US Join Date: Jun 2010 Posts: 177	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