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RSMD-repeat searcher and motif detector.

Mani U, Mahaganapathy V, Ravisankar S, Ramakrishnan SM - J Biomed Res (2014)

Bottom Line: The tool offers various features such as identifying motifs, repeats and identification of disease causing repeats.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu 613401, India.

ABSTRACT
The functionality of a gene or a protein depends on codon repeats occurring in it. As a consequence of their vitality in protein function and apparent involvement in causing diseases, an interest in these repeats has developed in recent years. The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level. Here, we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector (RSMD), which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency. The tool offers various features such as identifying motifs, repeats and identification of disease causing repeats. RSMD was designed to provide an easily understandable graphical user interface (GUI), for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science. GUI was developed using the scripting language Perl and its graphical module PerlTK. RSMD covers algorithmic foundations of computational biology by combining theory with practice.

No MeSH data available.


Frames of RSMD.4 row frames and 2 GUI frames. RSMD, Repeat Searcher and Motif Detector.
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f01: Frames of RSMD.4 row frames and 2 GUI frames. RSMD, Repeat Searcher and Motif Detector.

Mentions: As the relative ease Perl helps biologists to understand the language, it has been extensively employed along with its graphical module PerlTK in developing RSMD. The tool is divided into 2 main frames, and respectively sub-divided into 4 row frames and 2 graphical user interface (GUI) frames. The first row frame provides access to the major modules of the tool. The second row frame acts as the input panel. The third row frame contains legends for the pictorial representation of the sequences given as input. It also contains a feature to introduce mutations in the uploaded sequence. The final row frame displays the graphical representation of the input sequences. The first GUI frame displays various repeats along with its frequency of occurrence in the input sequence. Corresponding positions of the repeats are graphically represented in the second GUI frame (Fig. 1).


RSMD-repeat searcher and motif detector.

Mani U, Mahaganapathy V, Ravisankar S, Ramakrishnan SM - J Biomed Res (2014)

Frames of RSMD.4 row frames and 2 GUI frames. RSMD, Repeat Searcher and Motif Detector.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4197393&req=5

f01: Frames of RSMD.4 row frames and 2 GUI frames. RSMD, Repeat Searcher and Motif Detector.
Mentions: As the relative ease Perl helps biologists to understand the language, it has been extensively employed along with its graphical module PerlTK in developing RSMD. The tool is divided into 2 main frames, and respectively sub-divided into 4 row frames and 2 graphical user interface (GUI) frames. The first row frame provides access to the major modules of the tool. The second row frame acts as the input panel. The third row frame contains legends for the pictorial representation of the sequences given as input. It also contains a feature to introduce mutations in the uploaded sequence. The final row frame displays the graphical representation of the input sequences. The first GUI frame displays various repeats along with its frequency of occurrence in the input sequence. Corresponding positions of the repeats are graphically represented in the second GUI frame (Fig. 1).

Bottom Line: The tool offers various features such as identifying motifs, repeats and identification of disease causing repeats.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu 613401, India.

ABSTRACT
The functionality of a gene or a protein depends on codon repeats occurring in it. As a consequence of their vitality in protein function and apparent involvement in causing diseases, an interest in these repeats has developed in recent years. The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level. Here, we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector (RSMD), which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency. The tool offers various features such as identifying motifs, repeats and identification of disease causing repeats. RSMD was designed to provide an easily understandable graphical user interface (GUI), for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science. GUI was developed using the scripting language Perl and its graphical module PerlTK. RSMD covers algorithmic foundations of computational biology by combining theory with practice.

No MeSH data available.