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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.


Workflow of RSMD
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f02: Workflow of RSMD

Mentions: Maneuvering RSMD starts by selecting the required module from available options. On selecting the required module, users will be requested to upload the file which contains the input DNA or protein sequence (s) (.fasta or .aln file). On uploading the input file, users must select a suitable window length (1, 2, 3, 4, 5 or 6 amino acids/nucleotides). The entire analysis of input sequence is performed based on this window length. The sequence is searched for unique repeats, and its occurrence in the sequence is graphically depicted in GUI frames. The analysis of the sequence is performed and the presence of any motifs lying within is also depicted. All the motifs are obtained from PROSITE and other literature resources[15],[16]. The motifs are already stored in a database that enables easy and efficient use of toolkit. Disease-causing motifs can also be inferred from the uploaded sequence. Mutation module bases can be altered at various positions and the altered graphical map can be visualized. Each nucleotide or amino acid is represented with a unique color code, thus making the result easier to interpret. The detailed workflow of RSMD is shown in Fig. 2.


RSMD-repeat searcher and motif detector.

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

Workflow of RSMD
© Copyright Policy
Related In: Results  -  Collection

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

f02: Workflow of RSMD
Mentions: Maneuvering RSMD starts by selecting the required module from available options. On selecting the required module, users will be requested to upload the file which contains the input DNA or protein sequence (s) (.fasta or .aln file). On uploading the input file, users must select a suitable window length (1, 2, 3, 4, 5 or 6 amino acids/nucleotides). The entire analysis of input sequence is performed based on this window length. The sequence is searched for unique repeats, and its occurrence in the sequence is graphically depicted in GUI frames. The analysis of the sequence is performed and the presence of any motifs lying within is also depicted. All the motifs are obtained from PROSITE and other literature resources[15],[16]. The motifs are already stored in a database that enables easy and efficient use of toolkit. Disease-causing motifs can also be inferred from the uploaded sequence. Mutation module bases can be altered at various positions and the altered graphical map can be visualized. Each nucleotide or amino acid is represented with a unique color code, thus making the result easier to interpret. The detailed workflow of RSMD is shown in Fig. 2.

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.