How to use Glimmer to predict orf from Solexa contigs

anyone1985 · 09-06-2009, 03:11 AM

A genome about 6M has about 340 solexa contigs. I'd like to predict genes of each contig with the Glimmer. I don't know to do it from reference genome as training data or if i can use the long-orf to get training data from each contig. I wander if anyone do the same job and how i should do.

Mark · 09-06-2009, 05:35 AM

Yes, it is possible to do it using the long-orfs program, but I often juct go to NCBI and retrieve genes from their taxonomy browser of a closely related strain or species and use that to do my training. Be sure to use the -r flag when using build-icm. In my experience it helps a lot.

anyone1985 · 09-07-2009, 08:28 PM

Yes, glimmer with the training data is perfect. However, the contigs are parts of the genome. The training data maybe not suitable for the contig. Or I should do the training for every contig?

Quote:

Originally Posted by Mark

Yes, it is possible to do it using the long-orfs program, but I often juct go to NCBI and retrieve genes from their taxonomy browser of a closely related strain or species and use that to do my training. Be sure to use the -r flag when using build-icm. In my experience it helps a lot.

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09-06-2009, 03:11 AM	#1
anyone1985 Member Location: shanghai, chia Join Date: Mar 2009 Posts: 67	How to use Glimmer to predict orf from Solexa contigs A genome about 6M has about 340 solexa contigs. I'd like to predict genes of each contig with the Glimmer. I don't know to do it from reference genome as training data or if i can use the long-orf to get training data from each contig. I wander if anyone do the same job and how i should do.

09-06-2009, 05:35 AM	#2
Mark Member Location: Raleigh, NC Join Date: Nov 2008 Posts: 51	Yes, it is possible to do it using the long-orfs program, but I often juct go to NCBI and retrieve genes from their taxonomy browser of a closely related strain or species and use that to do my training. Be sure to use the -r flag when using build-icm. In my experience it helps a lot.