Finding genes with Glimmer3

Question

[alebuenosm]

Hello. I Apologize if this is the wrong place to ask it.

Well. I got a draft genome (after executing velvet and SSPACE). Now I am running glimmer3 to find genes in it and use the information on comparative genome studies and to annotate them.

The first step in running glimer is to execute the script "g3-from-scratch.csh" which is meant to find a training set of putative genes and generated the following files.

• prefix.train is the multifasta file of training sequences
• prefix.icm is the model
• prefix.upstream are the regions before the starts in <coords>
• prefix.motif is a PWM of the upstream regions
• prefix.detail is Glimmer3 output detail
• prefix.predict is Glimmer3 predictions

The second step (in which I got confused) is to use the script g3-from-traing.csh

This script requires my genome and a coordinate file train.coords. What got me confused is that the first step did not generated this train.coords file. Where should I get it from?

So I decided by myself to use prefix.train just because it has train in its name (OK.. very awful..). It looked like it worked. I'm not sure about the results as I used the file prefix.train just by chance.

Has someone of you used this software before? Am I doing the steps right way?

Thank you since now.