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. 2014 Sep;28(5):416-22.
doi: 10.7555/JBR.28.20130065. Epub 2014 Mar 20.

RSMD-repeat searcher and motif detector

Udayakumar Mani  1 , Vaidhyanathan Mahaganapathy  1 , Sadhana Ravisankar  1 , Sai Mukund Ramakrishnan  1
Affiliations

RSMD-repeat searcher and motif detector

Udayakumar Mani et al. J Biomed Res. 2014 Sep.

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.

Keywords: combination algorithm; computational biology; genomic sequence; motif; proteomic sequence; repeats.

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Figures

Fig. 1
Fig. 1. Frames of RSMD.
4 row frames and 2 GUI frames. RSMD, Repeat Searcher and Motif Detector.
Fig. 2
Fig. 2. Workflow of RSMD
Fig. 3
Fig. 3
Fig. 4
Fig. 4. Comparison of the graphical output between single sequence and multiple sequences input.
A: Single sequence (format: repeat(frequency)). B: Multiple sequences (format: repeat (frequency)[sequence_num]).
Fig. 5
Fig. 5. Case study depicting the RSMDs capability in identifying disease causing repeats.
Fig. 6
Fig. 6. Comparison of various tools with RSMD based upon computational speed in seconds.
See this image and copyright information in PMC

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