finding distances for unrelated sequences

Joe Felsenstein joe at removethispart.gs.washington.edu
Wed Dec 8 19:30:38 EST 2004


In article <cp7vat$oge$1 at mercury.rfcgr.mrc.ac.uk>,
Thomas Isenbarger  <isen at plantpath.wisc.edu> wrote:
>If the sequences were related and could be trimmed to the same length, I
>would do an alignment and then use phylip to create a distance matrix,
>but since my sequences are unrelated and cannot really be trimmed to the
>same length, I am at a loss for what to do.
>
>For a set with so many unrelated sequences of different lengths, the
>only thing I have been able to think of is an all-against-all BLAST to
>create a score matrix using the normalised bits score, but this gives
>high scores for similarities.  From there, the only thought I had was to
>use the reciprocal of the BLAST score as some perverse measure of
>distance.

BLAST assumes that alignment means something.  What does "similarity"
mean if there is no alignment?  I think you have to answer that
first before getting into specific algorithms.

-- 
Joe Felsenstein         joe at removethispart.gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 357730, Seattle, WA 98195-7730 USA
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