| URL: | http://www.cdfd.org.in/micas |
| Full name: | Microsatellite Analysis Server |
| Description: | MICAS is an interactive user-friendly web-based analysis server to find non-redundant microsatellites of a selected bacterial or archeal genome sequence. MICAS has been connected to the database MICdb3.0 that hosts microsatellites extracted from more than 5000 published prokaryotic genome sequences. The database hosts the microsatellite data of 4,772 bacterial and 271 archeal genome sequences (including plasmid sequences). |
| Year founded: | 2003 |
| Last update: | 2014 |
| Version: | 3.0 |
| Accessibility: |
Accessible
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| Country/Region: | India |
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| University/Institution: | University of Hyderabad |
| Address: | F-50, Laboratory of Computational Biology, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad (P.O. Central University), Prof. C.R.Road, Gachibowli, Hyderabad 500 046, India. |
| City: | Hyderabad |
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| Country/Region: | India |
| Contact name (PI/Team): | Hampapathalu A. Nagarajaram |
| Contact email (PI/Helpdesk): | han@cdfd.org.in |
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MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes. [PMID: 24536078]
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. |
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MICdb: database of prokaryotic microsatellites. [PMID: 12519959]
The MICdb (Microsatellites Database) (http://www.cdfd.org.in/micas) is a comprehensive relational database of non-redundant microsatellites extracted from fully sequenced prokaryotic genomes. The current version (1.0) of the database has been compiled from 83 genomes belonging to different phylogenetic groups. This database has been linked to MICAS, the web-based Microstatellite Analysis Server. MICAS provides a user-friendly front-end to systematically extract data on microsatellite tracts from genomes. The database contains the following information pertaining to the microsatellites: the regions (coding/non-coding, if coding, their GenBank annotations) containing microsatellite tracts; the frequencies of their occurrences, the size and the number of repeating motifs; and the sequences of the tracts. MICAS also provides an interface to Autoprimer, a primer design program to automatically design primers for selected microsatellite loci. |