Algorithm to find distant repeats in a single protein sequence

Banerjee, Nirjhar; Rangarajan, S.K.; Ranjani, C. Vasuki; Sowmiya, Govindaraj; Michael, Daliah; Balakrishnan, N; Sekar, K.

doi:10.6026/97320630003028

Cited by 4 publications

(2 citation statements)

References 14 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%

RPS: Repeats in Protein Sequences

et al. 2011

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“…As such, the sequence cannot be considered as a palindrome in the exact sense [4]. The importance of detecting such inverted repeats in both protein as well as nucleotide sequences and the methods used for the same has been elucidated before [5–7]. …”

Section: Introductionmentioning

confidence: 99%

A method to find palindromes in nucleic acid sequences

Anjana¹,

Shankar²,

Vaishnavi³

et al. 2013

Bioinformation

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Various types of sequences in the human genome are known to play important roles in different aspects of genomic functioning. Among these sequences, palindromic nucleic acid sequences are one such type that have been studied in detail and found to influence a wide variety of genomic characteristics. For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction. For example, both the strands i.e the strand going from 5' to 3' and its complementary strand from 3' to 5' must be complementary. A typical nucleotide palindromic sequence would be TATA (5' to 3') and its complimentary sequence from 3' to 5' would be ATAT. Thus, a new method has been developed using dynamic programming to fetch the palindromic nucleic acid sequences. The new method uses less memory and thereby it increases the overall speed and efficiency. The proposed method has been tested using the bacterial (3891 KB bases) and human chromosomal sequences (Chr-18: 74366 kb and Chr-Y: 25554 kb) and the computation time for finding the palindromic sequences is in milli seconds.

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