SD701 Open Directory

Top: Science: Biology: Bioinformatics: Online_Services: Homology_Detection:

» 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.




» GeneStream II - Sequence comparison and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch), from the IGH, Montpellier 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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