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  1. MICdb (View Publication)
    Full Name of the Resource : Prokaryotic microsatellites
    Resource Category : Databases -> Nucleotide Sequence Databases -> Coding and Coding DNA: Genes, Motifs and Regulatory Sites

    Brief Description : The MICdb (Microsatellites database) (http://www.cdfd.org.in/micas) is a comprehensive relational database of non-redundant microsatellites extracted from fully sequenced genomes. The current version (2.0) of the database is an enhanced and upgraded version compiled from 287 viral genomes as well as 129 prokaryotic genomes belonging to different phylogenetic groups and is loaded with tools and textual information so as to provide insights into structural and functional aspects of microsatellites. This database has been linked to MICAS2.0, the Web-based Microsatellite Analysis Server. MICAS provides an user-friendly front-end to systematically extract data on microsatellite tracts from hosted genomes. The database contains the following information pertaining to the microsatellites: The regions (coding/non-coding) containing microsatellite tracts, the frequencies of their occurrences, the size and the number of repeating motifs and the sequences of the tracts. Users are facilitated to query the database for details of microsatellite locations with respect to the protein coding/non-coding regions. Protein coding regions after translation are annotated with secondary structural information and positions of microsatellite tracts are shown in order to provide an insight into the possible structural changes due to microsatellite polymorphism. In the case of microsatellites occurring in the non-coding regions graphical illustrations are provided to show relative position of the microsatellite tracts with respect to the upstream and downstream coding regions. This will help in investigations on possible regulatory roles of microsatellites occurring close to protein coding regions (upstream or downstream). Sufficient textual information has been provided to help user navigation through the database and links to GenBank and Swissprot are provided to enhance information content pertaining to microsatellites. An interface to Autoprimer, a primer design program, has been provided to every microsatellite tract to compute suitable primers for PCR.
    Subject Area : Microsatellites; Prokaryotic Microsatellites


    Institute/s :
    Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
    Address of Institute/s :
    Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics (CDFD), ECIL Road, Nacharam, Hyderabad 500 076, India
    Country : India

    Associated Institutes :

    • Laboratory of Computational Biology and Bioinformatics Facility (EMBnet India Node), Centre for DNA Fingerprinting and Diagnostics (CDFD), ECIL Road, Nacharam, Hyderabad 500 076, India
    • Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics (CDFD), ECIL Road, Nacharam, Hyderabad 500 076, India

    Associated Country : India


    Authors/Contributors : Hampapathalu A. Nagarajaram
    Contact Email : han@cdfd.org.in
    Year : 2003
    Language : English

    Keywords : DNA Primers; Databases, Nucleic Acid; Genome; Information Storage and Retrieval; Microsatellite Repeats; Prokaryotic Cells; Software