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About msatfinderMsatfinder is a Perl script designed to allow the identification and characterization of microsatellites in a comparative genomic context. It can be freely downloaded for local use as used as GPL software. There is also an online manual, a discussion forum and an online interface where users can do searches in any number of DNA or protein sequences (as long as the maximum size of all sequences does not exceed 10MB). Nucleotide and amino acid sequences in GenBank, FASTA, EMBL and Swissprot formats are supported. Msatfinder is designed for use on *nix systems. Latest version: 2.0.9, last updated Wed Aug 9 15:06:39 BST 2006. See the CVS for information on changes. For more information please refer to the sections below: This project is hosted at Bioinformatics.Org. Please reference Msatfinder as: Thurston, M. I. and Field, D. 2005. Msatfinder: detection and characterisation of microsatellites. Distributed by the authors at http://www.genomics.ceh.ac.uk/msatfinder/. CEH Oxford, Mansfield Road, Oxford OX1 3SR. Introduction to microsatellitesMicrosatellite loci, short direct repeats of 1-6 bp, are among the most common and the most mutable DNA sequences found in nature (1). Since their discovery, the ability to use hypermutable microsatellites as molecular markers has revolutionised a range of disciplines from ecological and evolutionary genetics to forensics and genome mapping (2). Despite the fact that the vast majority of microsatellite loci are junk DNA accumulated through the mechanism of replication slippage (3), there are also well-known examples of microsatellites under selection, including the triplet-repeat expansion diseases of humans (4,5) and the contingency loci of pathogenic prokaryotes (6). Reasons for characterising the types of numbers of microsatellites in DNA sequences therefore include the potential development of molecular markers and the ability to study the role of these hypermutable repeats in gene and genome evolution. 1. Tautz, D., Trick, M., Dover, G.A. (1986) Nature, 322: 652-656. To the top. DownloadThe stable versions may be downloaded as one tar.gz or zip file containing the scripts, configuration file and some example files. Or, look at development versions hosted at bioinformatics.org. The CVS includes additional scripts that we are working on, but these are alpha software and therefore unsupported at present. Gentoo users may find an ebuild here, and Bio-Linux users will find a Debian package here. Of course, Bio-Linux users may simply... apt-get install msatfinder To the top. LinksThe following links may be of interest.
Also, there are various programs available for the detection of microsatellites &/or other repetitive sequences, and also databases of known microsatellites. Some of these are shown below. To the top. Msatfinder manualThere is a full manual that contains information on running the script as a stand alone application on your own machine, or on our on-line interface. The manual can be found here. To the top. Online interfaceFor those who don't need a local version, or don't have the facility to install it, we offer an on-line interface with almost identical functionality to the stand alone version. More information on each of the features can be found by clicking on the help icons ( To the top. FeedbackIf you have any questions or comments, please e-mail Paul Swift. He'd love to hear of any problems or suggestions for improvements. To the top.
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), which link to the relevant section of the manual.
