Smith-Waterman-Eggert including multiple subsequence alignment

Henrik Nielsen hnielsen at cbs.dtu.dk
Mon Sep 15 08:23:51 EST 1997


The LALIGN program of the FASTA package does this.  I quote from the
documentation:

LALIGN    Calculates the N-best local alignments using a rigorous
          algorithm.  (N=10 by default.) The algorithm was
          developed by Huang and Miller (X.  Huang and W.  Miller
          (1991) Adv. Appl. Math. 12:337-357), which is a
          linear-space version of an algorithm described by M. S.
          Waterman and M. Eggert (J.  Mol. Biol. 197:723-728).
          Like SSEARCH, LALIGN is rigorous, but also very slow.

The FASTA package is available from ftp.virginia.edu

Martijn Huynen wrote:
> 
> Hi
> 
> Does anybody have C-code for the modified version of the Smith-Waterman
> algorithm that also gives "non-intersecting similar subsequences"
> (published in J. Mol. Biol. (1987) 197, 723-728 by Waterman and Eggert)
> (the disadvantage of the original Smith-Waterman code is that it only
> gives one "hit" per pair of sequences, Blast does not have this disadvantage
> but is less rigorous/sensitive)
> 
> many thanks, Martijn
> 
> Martijn Huynen
> Biocomputing Group, EMBL
> Meyerhofstrasse 1
> 69012  Heidelberg, Germany
> tel: +49-6221-387372
> fax: +49-6221-387517

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| Henrik Nielsen, hnielsen at cbs.dtu.dk                                 |
| CBS - Center for Biological Sequence Analysis                       |
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