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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 administration module interface of MICAS3.0 using which the database administrator can add microsatellites of new genomes and can update the database easily.
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bau005-F5: The administration module interface of MICAS3.0 using which the database administrator can add microsatellites of new genomes and can update the database easily.

Mentions: As the number of genomes getting sequenced is increasing rapidly, most of the microsatellite databases are not updated and are outdated. To avoid this problem, MICdb3.0 is equipped with an admin module, a graphical user interface to update the microsatellite data of new genomes from time to time. The MICdb admin needs to login (with a valid user id and password) to the admin module for management of microsatellite and genome data in the database. The admin module can be used to add microsatellite data of new genomes as and when they become available at the NCBI genome repository, edit SSR data of an existing genome as well as delete the unwanted or redundant data from the database. The homepage of admin module displays the list of newly added/modified genomes of NCBI FTP server that are not present in MICdb with update buttons against those genomes. A single click will automatically download the FNA and PTT files of that genome to the MICAS server, submit the files to IMEx for SSR extraction and finally insert the records into the database. It has to be noted that as we use the annotations available at NCBI, they might include errors. Because annotations may also get updated at the NCBI, any such update is identified and the data are updated automatically by the admin module. The Edit feature of admin module has been provided to edit or make corrections to the meta-data and the microsatellite data of a genome. Similarly, the unwanted and redundant data in the database can be deleted directly using the delete option of admin module. A snapshot of the admin module can be found in the Figure 5.Figure 5.


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

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

The administration module interface of MICAS3.0 using which the database administrator can add microsatellites of new genomes and can update the database easily.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bau005-F5: The administration module interface of MICAS3.0 using which the database administrator can add microsatellites of new genomes and can update the database easily.
Mentions: As the number of genomes getting sequenced is increasing rapidly, most of the microsatellite databases are not updated and are outdated. To avoid this problem, MICdb3.0 is equipped with an admin module, a graphical user interface to update the microsatellite data of new genomes from time to time. The MICdb admin needs to login (with a valid user id and password) to the admin module for management of microsatellite and genome data in the database. The admin module can be used to add microsatellite data of new genomes as and when they become available at the NCBI genome repository, edit SSR data of an existing genome as well as delete the unwanted or redundant data from the database. The homepage of admin module displays the list of newly added/modified genomes of NCBI FTP server that are not present in MICdb with update buttons against those genomes. A single click will automatically download the FNA and PTT files of that genome to the MICAS server, submit the files to IMEx for SSR extraction and finally insert the records into the database. It has to be noted that as we use the annotations available at NCBI, they might include errors. Because annotations may also get updated at the NCBI, any such update is identified and the data are updated automatically by the admin module. The Edit feature of admin module has been provided to edit or make corrections to the meta-data and the microsatellite data of a genome. Similarly, the unwanted and redundant data in the database can be deleted directly using the delete option of admin module. A snapshot of the admin module can be found in the Figure 5.Figure 5.

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