Glimmer3.0 problem...

[Patrick]

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...

[Torst]

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

[Patrick]

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.