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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

The primer design interface of MICAS3.0 using which the user can prepare the input sequence for primer design with a flanking sequence of his/her choice.
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bau005-F6: The primer design interface of MICAS3.0 using which the user can prepare the input sequence for primer design with a flanking sequence of his/her choice.

Mentions: One of the primary needs of researchers studying SSRs is to design primer sequences for specific repeats. To facilitate primer design on the fly MICAS has been connected to the popular primer design software tool Primer3 (25). Each microsatellite repeat that is detected from a genome is hyperlinked to a primer design web interface (Figure 6). The microsatellite repeat along with the left and right flanking sequence is displayed and the sequence can be submitted as input to the primer3 web interface to design primer according to the user choice.Figure 6.


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

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

The primer design interface of MICAS3.0 using which the user can prepare the input sequence for primer design with a flanking sequence of his/her choice.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bau005-F6: The primer design interface of MICAS3.0 using which the user can prepare the input sequence for primer design with a flanking sequence of his/her choice.
Mentions: One of the primary needs of researchers studying SSRs is to design primer sequences for specific repeats. To facilitate primer design on the fly MICAS has been connected to the popular primer design software tool Primer3 (25). Each microsatellite repeat that is detected from a genome is hyperlinked to a primer design web interface (Figure 6). The microsatellite repeat along with the left and right flanking sequence is displayed and the sequence can be submitted as input to the primer3 web interface to design primer according to the user choice.Figure 6.

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