[Bio-software] Re: Advice about DNA alignment

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Tue Jan 8 14:44:07 EST 2008


On Jan 8, 12:08 pm, Gilad Lehmann <gila... from bgu.ac.il> wrote:
> Hello everybody, I need an advice.
>
> I want to align 30 homolog non-coding sequencess of  about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations.
>
> Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software?
> I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats.
>
> Thanks in advance,
> Giladý

Well, if you call them homolog than somehow you selected these
sequences based on similarity,  I assume. So if you deal with non-
coding regions close to a gene you may include 'anchors' -> extend
sequences to include i.e. coding exons.

>Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software?
 You will need something more advanced me thinks.

Check this paper http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1431#B15
and Aubergine:
http://zeus.cs.vu.nl/programs/aubergenewww/

Easy web-interface: MultiPipMaker
http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker

Shameless plug:
http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#DNA_alignment

Comments about tools accuracy/ease of use etc. will be greatly
appreciated ;-)

Darek Kedra
http://openwetware.org/wiki/Wikiomics



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