Biology: Bioinformatics: Online Services: Homology Detection

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	Home: Biology: Bioinformatics: Online Services: Homology Detection LINKS: WU-BLAST Archives http://blast.wustl.edu Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis. BLAST http://www.ncbi.nlm.nih.gov/BLAST/ NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases. GeneMatcher http://www.ch.embnet.org/software/GMFDF_form.html 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 http://xylian.igh.cnrs.fr/ 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 http://metameme.sdsc.edu/ Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego. The ISREC Group Servers http://www.isrec.isb-sib.ch/ 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. HMM library for all proteins of known structure http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ This is a server for structural superfamily assignments to protein sequences using Hidden Markov Models. The services included are: -homology searching -alignments -genome assignments GWBLAST http://www.imtech.res.in/raghava/gwblast/ Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities. Sequence Alignment and Modeling System http://www.cse.ucsc.edu/research/compbio/sam.html Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted online. ESPript http://prodes.toulouse.inra.fr/ESPript/ESPript/index.php Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry. Interactive Blast Query http://www.aridolan.com/biq/Query.aspx Utility for online manipulation of Blast results. Results organized in a table format.

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