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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 customized Primer3 interface of MICAS3.0 where the input sequence designed by the user is directly submitted and can be used to modify the various parameters to design primers.
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bau005-F7: The customized Primer3 interface of MICAS3.0 where the input sequence designed by the user is directly submitted and can be used to modify the various parameters to design primers.

Mentions: After selecting the sequence along with a flanking sequence of user's choice, the page will further be directed to a customized Primer3 web-interface (please see Figure 7) where the sequence is automatically loaded into the input field and user can select various primer designing parameters of primer3 so as to design primers of his/her choice. The flanking sequence size for each microsatellite can be changed dynamically. Instead of storing the flanking sequences in the database, we have included the entire sequence of each genome in a separate table so as to generate the flanking sequences on-the-fly.Figure 7.


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

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

The customized Primer3 interface of MICAS3.0 where the input sequence designed by the user is directly submitted and can be used to modify the various parameters to design primers.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bau005-F7: The customized Primer3 interface of MICAS3.0 where the input sequence designed by the user is directly submitted and can be used to modify the various parameters to design primers.
Mentions: After selecting the sequence along with a flanking sequence of user's choice, the page will further be directed to a customized Primer3 web-interface (please see Figure 7) where the sequence is automatically loaded into the input field and user can select various primer designing parameters of primer3 so as to design primers of his/her choice. The flanking sequence size for each microsatellite can be changed dynamically. Instead of storing the flanking sequences in the database, we have included the entire sequence of each genome in a separate table so as to generate the flanking sequences on-the-fly.Figure 7.

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