On Thu, Apr 14, 2011 at 5:13 PM, Brad Chapman chapmanb@50mail.com 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_islan...
Brad
Good idea Brad :)
Now why does a tool search on the public Galaxy instance for GC not suggest this tool?
Name: geecee Description: Calculates fractional GC content of nucleic acid sequences
Does this mean the description isn't searched? It would seem like a sensible idea to me to include that...
Searching for "geecee" works, but unless you're familiar with this EMBOSS tool no-one will think of that.
Peter