Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to...

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the ...

A characteriation of continuity of the $p$-$Lambda$-variation function is given and the Helly's selection principle for $Lambda BV^{(p)}$ functions is established. A characterization of the inclusion of Waterman-Shiba classes into classes of functions with given integral modulus of continuity is given. A useful estimate on modulus of variation of functions of class $Lambda BV^{(p)}$ is found.

Algorithms for estimating similarity between two macromolecular sequences are of profound importance for molecular biology. The standard methods utilize so-called primary structure, that is a string of characters denoting the sequence of monomers in hetero-polymer. These methods find the substrings of maximal similarity, as defined by the so-called similarity matrix, for a pair of two molecules...

With an aim to understand the information encoded by DNA sequences, databases containing large amount of DNA sequence information are frequently compared and searched for matching or near-matching patterns. This kind of similarity calculation is known as sequence alignment. To date, the most popular algorithms for this operation are heuristic approaches such as BLAST and FASTA which give high s...

Sequence alignment is a task that calculates the degree of similarity between two sequences. Given a query sequence, finding a database sequence which is most similar to the query by sequence alignment is the first step in bioinformatics research. The first sequence alignment algorithm was proposed by Needleman and Wunsch. They got the optimal global alignment by using dynamic programming metho...

Article history: Received 15 December 2008 Available online 3 March 2010 Submitted by D. Waterman

a characteriation of continuity of the $p$-$lambda$-variation function is given and the helly's selection principle for $lambda bv^{(p)}$ functions is established. a characterization of the inclusion of waterman-shiba classes into classes of functions with given integral modulus of continuity is given. a useful estimate on modulus of variation of functions of class $lambda bv^{(p)}$ is found.