Tandem repeats over the edit distance

TRedD—A database for tandem repeats over the edit distance

A 'tandem repeat' in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem ...

An 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...

Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation

Using our techniques for extracting approximate non-tandem repeats[1] on well constructed maximal models, we derive an algorithm to find common motifs of length P that occur in N sequences with at most D differences under the Edit distance metric. We compare the effectiveness of our algorithm with the more involved algorithm of Sagot[17] for Edit distance on some real sequences. Her method has ...

A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment

In spite of the recognized importance of tandem duplications in genome evolution, commonly adopted sequence comparison algorithms do not take into account complex mutation events involving more than one residue at the time, since they are not compliant with the underlying assumption of statistical independence of adjacent residues. As a consequence, the presence of tandem repeats in sequences u...

Editorial: Could Speciation Across Evolution be Governed by Genetic Switch Codes at Short Tandem Repeats?