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MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes.

Mudunuri SB, Patnana S, Nagarajaram HA - Database (Oxford) (2014)

Bottom Line: 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.All the query results and graphs can be exported in different formats so that the users can use them for further analysis.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science & Engineering, Grandhi Varalakshmi Venkatarao Institute of Technology, Bhimavaram, Andhra Pradesh 534 207, India, Training & Delivery Department, TalentSprint Educational Services, IIIT Campus, Hyderabad, Andhra Pradesh 500 032, India and Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Andhra Pradesh 500 001, India.

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.

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Related in: MedlinePlus

A snapshot of Advanced Search of MICAS and the results page.
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bau005-F3: A snapshot of Advanced Search of MICAS and the results page.

Mentions: To facilitate users for getting repeats based on specific search criteria, MICAS3.0 has been provided with an advanced search module. Using the advanced search module, users can select a particular genome of interest and also specify his/her search criteria and filter repeats accordingly. Advanced search module can filter repeats of a particular size (mono, tri, tetra, etc.,); can get repeats of a particular pattern (CAG, Poly A etc.); can set the minimum repeat number of each motif size; and can filter repeats of only coding or non-coding regions. Moreover, the advanced search module allows you to define the output format (HTML, Excel, CSV or Text) and also sort results based on motif, motif-size or tract length (Figure 3).Figure 3.


MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes.

Mudunuri SB, Patnana S, Nagarajaram HA - Database (Oxford) (2014)

A snapshot of Advanced Search of MICAS and the results page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3926409&req=5

bau005-F3: A snapshot of Advanced Search of MICAS and the results page.
Mentions: To facilitate users for getting repeats based on specific search criteria, MICAS3.0 has been provided with an advanced search module. Using the advanced search module, users can select a particular genome of interest and also specify his/her search criteria and filter repeats accordingly. Advanced search module can filter repeats of a particular size (mono, tri, tetra, etc.,); can get repeats of a particular pattern (CAG, Poly A etc.); can set the minimum repeat number of each motif size; and can filter repeats of only coding or non-coding regions. Moreover, the advanced search module allows you to define the output format (HTML, Excel, CSV or Text) and also sort results based on motif, motif-size or tract length (Figure 3).Figure 3.

Bottom Line: 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.All the query results and graphs can be exported in different formats so that the users can use them for further analysis.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science & Engineering, Grandhi Varalakshmi Venkatarao Institute of Technology, Bhimavaram, Andhra Pradesh 534 207, India, Training & Delivery Department, TalentSprint Educational Services, IIIT Campus, Hyderabad, Andhra Pradesh 500 032, India and Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Andhra Pradesh 500 001, India.

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.

Show MeSH
Related in: MedlinePlus