An algorithm to find distant repeats in a pair of protein sequences

Sabarinathan, Radhakrishnan; Banerjee, Nirjhar; Sekar, K.

doi:10.1016/j.patrec.2010.04.010

Cited by 1 publication

(1 citation statement)

References 17 publications

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“…A PAM 250 matrix (Dayhoff et al, 1978) works well for weighting purposes, because at this evolutionary distance, only one in five amino acid residues remains unchanged (250 mutation events for every 100 amino acids). The two recently developed algorithms for finding distant repeats in protein sequences (Banerjee, Sarani et al, 2008;Sabarinathan et al, 2010) are implemented in the web server.…”

Section: Computing Server To Find Distant Repeatsmentioning

confidence: 99%

RPS: Repeats in Protein Sequences

et al. 2011

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Repeats are two or more contiguous segments of amino acid residues that are believed to have arisen as a result of intragenic duplication, recombination and mutation events. These repeats can be utilized for protein structure prediction and can provide insights into the protein evolution and phylogenetic relationship. Therefore, to aid structural biologists and phylogeneticists in their research, a computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats (of varying lengths) in protein sequences. In addition, users can check the frequency of occurrence of the repeats in sequence databases such as the Genome Database, PIR and SWISS‐PROT and among the protein sequences available in the Protein Data Bank archive. Furthermore, users can view the three‐dimensional structure of the repeats using the Java visualization plug‐in Jmol. The proposed computing resource can be accessed over the World Wide Web at http://bioserver1.physics.iisc.ernet.in/rps/.

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Section: Computing Server To Find Distant Repeatsmentioning

confidence: 99%