Speeding up the detection of evolutive tandem repeats

Speeding up the detection of evolutive tandem repeats

We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. MFCS’02: the 27th Internat. Symp. Mathematical Foundations of Computer Science, Warszawa, Otwock, Poland, August 2002, Lecture Notes in Computer Science, Vol. 2420, Springer, Berlin, pp. 292–304) which consist in a series of almost contiguous copies having the following property: the Hamming distance betwe...

A Linear Algorithm for the Detection of Evolutive Tandem Repeats

Abstra t. We present here a linear algorithm for the dete tion of evolutive tandem repeats. An evolutive tandem repeat onsists in a series of almost ontiguous opies, every opy being similar (using Hamming distan e in this arti le) to its prede essor and su essor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where ea h opy has to be in a nei...

A Linear Algorithm for the Dete tion of Evolutive Tandem Repeats

Abstra t. We present here a linear algorithm for the dete tion of evolutive tandem repeats. An evolutive tandem repeat onsists in a series of almost ontiguous opies, every opy being similar (using Hamming distan e in this arti le) to its prede essor and su essor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where ea h opy has to be in a nei...

Speeding Up Parallelism Detection for Attribute Grammars

mreps: efficient and flexible detection of tandem repeats in DNA

The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms and plays an important role in genomic fingerprinting. In this paper, we describe mreps, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. mreps is ...