Retention Time Alignment of LC/MS Data by a Divide-and-Conquer Algorithm

Kart: a divide-and-conquer algorithm for NGS read alignment

Motivation Next-generation sequencing (NGS) provides a great opportunity to investigate genome-wide variation at nucleotide resolution. Due to the huge amount of data, NGS applications require very fast and accurate alignment algorithms. Most existing algorithms for read mapping basically adopt seed-and-extend strategy, which is sequential in nature and takes much longer time on longer reads. ...

A Divide-and-Conquer Discretization Algorithm

The problem of real value attribute discretization can be converted into the reduct problem in the Rough Set Theory, which is NP-hard and can be solved by some heuristic algorithms. In this paper we show that the straightforward conversion is not scalable and propose a divide-and-conquer algorithm. This algorithm is fully scalable and can reduce the time complexity dramatically especially while...

A Divide and Conquer Approach to Multiple Alignment

We present a report on work in progress on a divide and conquer approach to multiple alignment. The algorithm makes use of the costs calculated from applying the standard dynamic programming scheme to all pairs of sequences. The resulting cost matrices for pairwise alignment give rise to secondary matrices containing the additional costs imposed by fixing the path through the dynamic programmin...

A Versatile Divide and Conquer Technique for Optimal String Alignment

Common string alignment algorithms such as the basic dynamic programming algorithm (DPA) and the time efficient Ukkonen algorithm use quadratic space to determine an alignment between two strings. In this paper we present a technique that can be applied to these algorithms to obtain an alignment using only linear space, while having little or no effect on the time complexity. This new technique...

Divide and Conquer for Linear Expected Time