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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

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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