Abstract
The MICdb is a comprehensive relational database of perfect microsatellites extracted from completely sequenced and annotated genomes of bacteria and archaea. The current version MICdb3.0 is an updated and revised version of MICdb2.0. As compared with the previous version MICdb2.0, the current release is significantly improved in terms of much larger coverage of genomes, improved presentation of queried results, user-friendly administration module to manage Simple Sequence Repeat (SSR) data such as addition of new genomes, deletion of obsolete data, etc., and also removal of certain features deemed to be redundant. The new web-interface to the database called Microsatellite Analysis Server (MICAS) version 3.0 has been improved by the addition of powerful high-quality visualization tools to view the query results in the form of pie charts and bar graphs. All the query results and graphs can be exported in different formats so that the users can use them for further analysis. MICAS3.0 is also equipped with a unique genome comparison module using which users can do pair-wise comparison of genomes with regard to their microsatellite distribution. The advanced search module can be used to filter the repeats based on certain criteria such as filtering repeats of a particular motif/repeat size, extracting repeats of coding/non-coding regions, sort repeats, etc. The MICdb database has, therefore, been made portable to be administered by a person with the necessary administrative privileges. The MICdb3.0 database and analysis server can be accessed for free from www.cdfd.org.in/micas.Database URL: http://www.cdfd.org.in/micas
Highlights
Microsatellites, known as Simple Sequence Repeats or Short Tandem Repeats, are the tandem repetitions of nucleotide motifs of size 1–6 bp [1]
MICdb is linked to a graphical interface called Microsatellite Analysis Server (MICAS) using which the database is queried [20]
MICdb3.0, like its previous version, does not host the repeat data of viruses, as a separate and exclusive microsatellite database exists for viral genomes named Viral Microsatellite Database (VMD) [17]
Summary
Microsatellites, known as Simple Sequence Repeats or Short Tandem Repeats, are the tandem repetitions of nucleotide motifs of size 1–6 bp [1]. MICdb is a relational database of perfect microsatellites extracted from known prokaryotic genomes developed by us. MICdb is linked to a graphical interface called Microsatellite Analysis Server (MICAS) using which the database is queried [20].
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