[EMBOSS] Is there any way to use water or needle to do an all-to-all alignment?

[Thomas Girke]

Here is a simple shell loop to run needle or water in all-against-all
mode. It expects the sequences in separate files which can easily be
done with: 
	seqret my_fasta fasta::test -ossingle

The actual shell loop looks like this:

	for i in *.fasta; do for j in *.fasta; do needle $i $j stdout 
	-gapopen 10.0 -gapextend 0.5 >> my_needle_file; done; done;

This commands loops over all *.fasta files in the current directory 
and appends the results to the output file 'my_needle_file'.

Thomas



On Fri 11/18/05 16:29, Jon Ison wrote:
> Hi Zhiqiang Ye
> 
> Have a look at the "allversusall" program in the EMBASSY "DOMALIGN" package:
> 
> http://emboss.sourceforge.net/apps/allversusall.html
> 
> It's beta software so go steady.  If it doesn't do exactly what you want
> I'll gladly adapt it for you.  Let us know how you get on.
> 
> Cheers
> 
> Jon
> 
> 
> > Hi, all
> >    I want to do all-to-all pairwise comparison frequently. I have a
> > fasta file "total.fasta" containing many sequences, I want to get the
> > their pairwise comparison identities.  I don't want to split it to
> > single fasta files and then needle them to the "total.fasta"  since I
> > have to do this frequently.  Could needle or water be used for
> > all-to-all alignment directly?  Just like blast.
> >
> >     Thank you very much.
> >
> > --
> > Zhiqiang Ye
> > PHD candidate
> > College of Lifesciences, Center for Bioinformatics
> > Peking University, Beijing.
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at emboss.open-bio.org
> > http://newportal.open-bio.org/mailman/listinfo/emboss
> >
> 
> 
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-- 
Thomas Girke
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