We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize these regions that allow marked improvements in both specificity and sensitivity over existing techniques for sequence alignment. For any such characterization, which we call a vector seed, we give...

bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. many computational algorithms have been applied for solving the sequence alignment problem. dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods applied t...

MOTIVATION Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, Smi...

The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the ...

Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the...

We are interested in detecting homologous genomic DNA sequences with the goal of locating approximate inverted, interspersed, and tandem repeats. Standard search techniques start by detecting small matching parts, called seeds, between a query sequence and database sequences. Contiguous seed models have existed for many years. Recently, spaced seeds were shown to be more sensitive than contiguo...

Optimal spaced seeds were introduced by the theoretical computer science community to bioinformatics to effectively increase homology search sensitivity. These seeds are serving many homology queries daily. However the computational complexity of finding the optimal spaced seeds remains to be open. In this paper, we prove that computing hit probability of a spaced seed in a uniform homology reg...