STAR: an algorithm to Search for Tandem Approximate Repeats
نویسندگان
چکیده
منابع مشابه
STAR: an algorithm to Search for Tandem Approximate Repeats
MOTIVATION Tandem repeats consist in approximate and adjacent repetitions of a DNA motif. Such repeats account for large portions of eukaryotic genomes and have also been found in other life kingdoms. Owing to their polymorphism, tandem repeats have proven useful in genome cartography, forensic and population studies, etc. Nevertheless, they are not systematically detected nor annotated in geno...
متن کاملAn Algorithm for Approximate Tandem Repeats
A perfect single tandem repeat is defined as a nonempty string that can be divided into two identical substrings, e.g., abcabc. An approximate single tandem repeat is one in which the substrings are similar, but not identical, e.g., abcdaacd. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of lengt...
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We study the problem of approximate non-tandem repeat extraction. Given a long subject string S of length N over a finite alphabet Sigma and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact rep...
متن کاملAn Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats
An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X ("motifs") interspersed with one another. NTRs fall into a class of repetitive structures broadly known as subrepeats. NTRs have been found in real DNA sequences and are expected to be important in evolutionary biology, both in understanding e...
متن کاملExhaustive whole-genome tandem repeats search
MOTIVATION Approximate tandem repeats (ATR) occur frequently in the genomes of organisms, and are a source of polymorphisms observed in individuals, and thus are of interest to those studying genetic disorders. Though extensive work has been done in order to identify ATRs, there are inherent limitations with the current approaches in terms of the number of pattern sizes that can be searched or ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bth335