Additional
Information: This category is for online services which use algorithms to find genes or proteins homologous to input DNA or amino acid sequences. The most common algorithms used are based on a method called BLAST.
Homology Detection Sites:
Interactive Blast Query Interactive Blast Query: Utility for online manipulation of Blast results. Results organized in a table format. (Homology Detection) http://www.aridolan.com/biq/Query.aspx
HMM library for all proteins of known structure 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 (Homology Detection) http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
WU-BLAST Archives WU-BLAST Archives: Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis. (Homology Detection) http://blast.wustl.edu
Meta-MEME v2.0.1 Meta-MEME v2.0.1: Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego. (Homology Detection) http://metameme.sdsc.edu/
ESPript ESPript: Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry. (Homology Detection) http://prodes.toulouse.inra.fr/ESPript/ESPript/index.php
GWBLAST GWBLAST: Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities. (Homology Detection) http://www.imtech.res.in/raghava/gwblast/
The ISREC Group Servers 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. (Homology Detection) http://www.isrec.isb-sib.ch/
GeneMatcher 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. (Homology Detection) http://www.ch.embnet.org/software/GMFDF_form.html
BLAST BLAST: NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases. (Homology Detection) http://www.ncbi.nlm.nih.gov/BLAST/
GeneStream II GeneStream II: Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch) - from the IGH, Montpellier FR. (Homology Detection) http://xylian.igh.cnrs.fr/
Sequence Alignment and Modeling System 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. (Homology Detection) http://www.cse.ucsc.edu/research/compbio/sam.html
Additional
Information: This category is for online services which use algorithms to find genes or proteins homologous to input DNA or amino acid sequences. The most common algorithms used are based on a method called BLAST.
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