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Chromas & Co.

Gary Williams gwilliam at hgmp.mrc.ac.uk
Fri Jan 10 04:35:03 EST 2003

In article <20030108082352.3e8364cc.mathog at caltech.edu>,
David Mathog <mathog at caltech.edu> wrote:
>On 7 Jan 2003 12:17:04 -0000
>Rudi.Effe at gmx.de (Rudi Effe) wrote:
>> Given a original sequence of a bacteria (ca. 700 letters), I am probing
>> a series of slight mutations and just keeping track of the few positions
>> where the deviations occur. Is there a tool that just returns the
>> positons (like 64, 223, 511) or, even better, does a multiple comparism
>> and draws histograms of the positions found?
>Several tools can do the alignment, for instance, clustalw.  The
>trick is to put in your mutants and then enough identical copies
>of the wild type sequence so that it will always emerge as the consensus
>sequence.  (Worst case, 1 more than all the mutant sequences).  Then
>view the resulting alignment showing only differences from the consensus. 
>GCG's PRETTY can do this (-differences) as can the EMBOSS "showalign".

In showalign, you can specify which sequence you want to take as the
reference sequence to comapre to when displaying differences, you do not
need to use the consensus as the reference.  This means that you don't
have to put in the multiple copies of the wildtype. 

showalign -refseq 'wildtype' -show=Non-identities

The -refseq qualifier can take either the ordinal number of the sequence
in the alignment or the ID name (i.e.  'wildtype' in the example above)
of the required sequence. 

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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