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Article #2593Re: Advice about DNA alignment
From: darked
Date: Tue, 08 Jan 2008 19:44
Date: Tue, 08 Jan 2008 19:44
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On Jan 8, 12:08 pm, Gilad Lehmann <gila...@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, > GiladοΏ½ 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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