Chromas & Co.

David Mathog mathog at caltech.edu
Thu Jan 9 05:44:10 EST 2003


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".
(-show=Non-identities).

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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