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Fast guide:

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Homology Detection:

DNA structural software

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• BLAST - NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
• ESPript - Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry.
• 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.
• GWBLAST - Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities.
• HMM library for all proteins of known structure - This is a server for structural superfamily assignments to protein sequences using Hidden Markov Models. The services included are: -homology searching -alignments -genome assignments
• Interactive Blast Query - Utility for online manipulation of Blast results. Results organized in a table format.
• 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.
• Meta-MEME - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
• mreps : maximal tandem repeats search - Open source tool for identifying serial repeats (tandem repeats) in DNA sequences.
• PatternHunter - Commercial general homology search software significantly faster than BLAST.
• Sequence Alignment and Modeling System - Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted online.
• WU-BLAST Archives - Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.

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