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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

List of all tri-nucleotide microsatellites of E. coli HS genome along with a snapshot window of a particular microsatellite repeat along with its summary and flanking sequence.
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bau005-F2: List of all tri-nucleotide microsatellites of E. coli HS genome along with a snapshot window of a particular microsatellite repeat along with its summary and flanking sequence.

Mentions: The list of SSRs are displayed neatly in tabular format with details such as the repeat motif, iterations, start and end co-ordinates of each SSR, nucleotide composition of each SSR, a link to the protein information if the SSR falls in coding regions and an option to design primer separately for each SSR. Clicking on the co-ordinates will display the complete SSR sequence along with a flanking sequence and summary information of that SSR (Figure 2). An option to export the total SSRs into various formats (.xls, .csv and .txt) has also been provided using which users can download the SSRs and further use them in their analysis.


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

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

List of all tri-nucleotide microsatellites of E. coli HS genome along with a snapshot window of a particular microsatellite repeat along with its summary and flanking sequence.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bau005-F2: List of all tri-nucleotide microsatellites of E. coli HS genome along with a snapshot window of a particular microsatellite repeat along with its summary and flanking sequence.
Mentions: The list of SSRs are displayed neatly in tabular format with details such as the repeat motif, iterations, start and end co-ordinates of each SSR, nucleotide composition of each SSR, a link to the protein information if the SSR falls in coding regions and an option to design primer separately for each SSR. Clicking on the co-ordinates will display the complete SSR sequence along with a flanking sequence and summary information of that SSR (Figure 2). An option to export the total SSRs into various formats (.xls, .csv and .txt) has also been provided using which users can download the SSRs and further use them in their analysis.

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