[Bioperl-l] SWAT Implementation

Aaron J. Mackey amackey at pcbi.upenn.edu
Sat Dec 4 18:17:50 EST 2004

The FASTA search suite includes the "reference" implementation of 
Smith-Waterman, called "ssearch"; ssearch in fact implements the SWAT 
optimization, while the program "osearch" implements the "traditional" 
S-W algorithm.  You can find the code for each in dropnsw.c (normal 
smith waterman) and dropgsw.c (green smith waterman) from the FASTA 
pacakge (ftp://ftp.virginia.edu/pub/fasta/).


denise dolan wrote:
> Hi. I am working on a program for my thesis. It uses the smith-waterman 
> algorithm and i want to use the SWAT implementation to speed it up. I 
> can't seem to find an accurate description or code for it and was 
> wondering if anyone could help. Would be really grateful of any info as 
> i am totally stuck. Thanks 
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