Web Directory

» BLAST
   Suite of alignment tools to detect conserved sequences, similar domain architecture, gene expression profiles, and SNP using protein or nucleotide targets. Includes support and archiving of strategies at NCBI, Bethesda, Maryland.
   http://blast.ncbi.nlm.nih.gov/

» ESPript
   Formatting of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry.
   http://espript.ibcp.fr/ESPript/ESPript/

» GWBLAST
   Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities.
   http://www.imtech.res.in/raghava/gwblast/

» 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.
   http://www.ch.embnet.org/software/GMFDF_form.html

» GeneStream II
   Sequence comparison and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch), from the IGH, Montpellier FR.
   http://xylian.igh.cnrs.fr/

» 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
   http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

» Interactive Blast Query
   Utility for online manipulation of Blast results. Results organized in a table format.
   http://www.aridolan.com/biq/Query.aspx

» Meta-MEME
   Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
   http://metameme.sdsc.edu/

» PatternHunter
   Commercial general homology search software significantly faster than BLAST.
   http://www.bioinformaticssolutions.com/products/ph/

» 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.
   http://www.cse.ucsc.edu/research/compbio/sam.html

» 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.
   http://www.isrec.isb-sib.ch/

» WU-BLAST Archives
   Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.
   http://blast.wustl.edu

» mreps : maximal tandem repeats search
   Open source tool for identifying serial repeats (tandem repeats) in DNA sequences.
   http://bioinfo.lifl.fr/mreps/