Thanks for pointing this out, Brad. Both geecee and infoseq are in fact available on Galaxy under EMBOSS section.

Guru.

On Thu, Apr 14, 2011 at 12:13 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_islands_group.html

Brad

--
Graduate student, Bioinformatics and Genomics

Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
guru@psu.edu

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