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Homology Detection

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DNA structural software (25)

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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 comparison and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch), from the IGH, Montpellier FR.

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

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

http://www.imtech.res.in/raghava/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.

http://www.ncbi.nlm.nih.gov/BLAST/ - http://www.ncbi.nlm.nih.gov/BLAST/
NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.

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

Meta-MEME - 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.

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

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

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.

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.

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

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