Hello Maxim,
Using the tools in EMBOSS can help with these type of text manipulations
if you find the basic Text Manipulations tools do not do exactly what
you want. For #1, use EMBOSS->biosed to perform substitutions. For #2,
use EMBOSS->fuzznuc. A workflow for #2, using your data, is here as an
example:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/wf-advanced-text-manipula...
No stupid questions! Very glad we could help you to get going. Apologies
for the late reply.
Best,
Jen
Galaxy team
On 11/29/10 6:25 AM, Maxim Ivanov wrote:
Hello,
Sorry for possibly stupid question. Could you advise me whether there are any ways in
Galaxy to perform specific manipulations on DNA sequences like:
"Substitute all Gs to Cs (except for CG dinucleotides)":
Input: chr1 9078238 9078358 Bait1
ACGAGAGACTGGACCTAGCGTGACCTCTGCGGCTGCCGGT
Output: chr1 9078238 9078358 Bait1
ACGACACACTCCACCTACCGTCACCTCTCCGCCTCCCGCT
or like:
"Count the number of CG dinucleotides"
Input: chr1 9078238 9078358 Bait1
ACGAGAGACTGGACCTAGCGTGACCTCTGCGGCTGCCGGT
Output: chr1 9078238 9078358 Bait1 ACGAGAGACTGGACCTAGCGTGACCTCTGCGGCTGCCGGT
4
using built-in tools (e.g. specific expressions in the "Compute" tool), or this
task cannot be done without programming skills?
Thank you in advance!
With respect,
Maxim Ivanov
Dept. of Physiology and Pharmacology
Karolinska Institutet
Stockholm, Sweden
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