SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Reply
 
Thread Tools
Old 03-20-2009, 12:11 AM   #1
Patrick
Member
 
Location: Malaysia

Join Date: Mar 2009
Posts: 27
Default Glimmer3.0 problem...

Hi,
Glimmer is a collection of programs for identifying genes in microbial DNA sequences.
For running the glimmer requires 4 steps:
1. long-orfs USAGE: ./long-orfs <genome-file> [options]
2. extract Usages: extract genome_file coord_file
3. build-icm USAGE: build-icm [options]
4. glimmer3 USAGE: glimmer3 <genome-file> <icm-file> [options]
For example, I have one file named as tpall.fna. What command line I should type for running the glimmer3.0 step by step?

ps: what is the general command line that we should type to get use the Glimmer3.0 to find out the gene in microbial DNA sequences.

Thanks a lot...
Patrick is offline   Reply With Quote
Old 03-28-2009, 05:41 PM   #2
Torst
Senior Member
 
Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275
Default

Patrick,

You should look in the scripts/ subdirectory of the Glimmer distribution. It contains scripts like g3-from-scratch.sh and g3-iterated.sh which do all the tricky steps for you. Essentially you can just feed it your sequence and get out a gene prediction report.

--Torsten
Torst is offline   Reply With Quote
Old 03-29-2009, 04:30 PM   #3
Patrick
Member
 
Location: Malaysia

Join Date: Mar 2009
Posts: 27
Default

Quote:
Originally Posted by Torst View Post
Patrick,

You should look in the scripts/ subdirectory of the Glimmer distribution. It contains scripts like g3-from-scratch.sh and g3-iterated.sh which do all the tricky steps for you. Essentially you can just feed it your sequence and get out a gene prediction report.

--Torsten
Hi, thanks a lot.
I finally solve this problem already. Really thanks for your advise.
Patrick is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO