Hi Brad,

These tools are also in galaxy under the EMBOSS section. "geecee" will tell you the percentage of GC in FASTA sequences. It basically outputs the sequence name and then the GC content as below:

#Sequence   GC content
Sequence1  0.44
Hope this helps!

Tychele


On Apr 14, 2011, at 12:13 PM, Brad Chapman wrote:

Peter and Guru;

[Computing GC]

I'll be working with simple sequence files (FASTA, or even FASTQ,
SFF, etc) rather than BED files, but I'll keep that in mind.

Emboss has some utilities that do this. infoseq and geecee, and
there are also programs for exploring CpG islands:

http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/nucleic_cpg_islands_group.html

Brad
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to