Optimal seed solver: optimizing seed selection in read mapping.

ABSTRACT:

Motivation

Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the ability of the mapper in selecting less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds.

Results

We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently

SUBMITTER: Xin H 

PROVIDER: S-EPMC6363230 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature