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
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