[EMBOSS] using emma: where to put clustalw

[Gary Williams, Tel 01223 494522]

Some alternate multiple alignment programs for nucleotide sequences on
the web are at:

http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-mult.html

I would recommend DIALIGN

Gary


Robin Colgrove wrote:
> 
> Thanks to all for suggestions.
> Just putting clustalw in /usr/local/bin did the trick.
> 
> Now, I need to figure out why emma/clustalw is giving me such bad
> alignments.
> Since I only had 4 sequences, I ended up aligning them pairwise with
> needle, then pieced together the full alignment in vi, but this is not
> going to fly as the number of sequences increases. The online tool I
> use for quick alignments (
> http://prodes.toulouse.inra.fr/multalin/multalin.html ) does fine, but
> the same fasta file sent either to emma or directly to clustalw gives
> obviously wrong alignments, even though the nucleotide sequences are
> highly homologous.
> 
> thanks again
> 
> robin
> 
> On Apr 12, 2005, at 10:17 AM, Robin Colgrove wrote:
> 
> >
> > Hello.
> >
> > I was trying to use emma for a multiple sequence alignment of dna
> > sequencing reads, but it complained that it could not find clustalw. I
> > could not find any mention of clustalw on the EMBOSS page, so I got a
> > copy from the clustalw homepage and -not knowing where to place it-
> > tried the /usr/local/share/ EMBOSS/acd directory. That didn't work,
> > and emma gives the error:
> >
> >    EMBOSS An error in ajsys.c at line 398:
> > cannot find program 'clustalw'
> >
> > Looking in the emma.acd and ajsys.c files, I can't find any guidance.
> >
> > Does anyone know how this is supposed to work?
> > Alternatively, is there another good way to do multiple sequence
> > alignment?
> > Looking ahead, I do not find any obvious way to do contig assembly, a
> > la Phrap, or CAP.
> >
> > thanks
> >
> > robin colgrove
> >

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk