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Biology WorkBench - A online interface for searching protein and nucleic acid sequence databases and analyzing sequence data - from the Univ. of Illinois.
 
DeCypher II - Smith-Waterman protein and nucleic acid database search program - from TimeLogic Corp.
 
GeneMatcher - Access to Smith-Waterman-based FDF sequence comparison program, with excellent explanation of when to use it vs. BLAST - from the Univ. of Lausanne, FR.
 
GeneStream II - Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch) - from the IGH, Montpellier FR.
 
Meta-MEME v2.0.1 - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
 
NCBI BLAST - BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
 
SUPERFAMILY HMM library for Structural Assignments to protein sequences and Genomes - This server is a Hidden Markov Model library providing 3 services: sequence searching, sequence alignments and genome assignments.
 
The ISREC Group Servers - Detection and assessment of similarity between distantly related sequences by means of a variety of remotely-executable software - from the Swiss Inst. for Experimental Cancer Research.
 
WU-BLAST Archives - Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.
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