An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

ABSTRACT:

Background

Oligonucleotide design is known as a time-consuming work in bioinformatics. In order to accelerate and be efficient the oligonucleotide design process, one of widely used approach is the prescreening unreliable regions using a hashing (or seeding) algorithm. Since the seeding algorithm is originally proposed to increase sensitivity for local alignment, the specificity should be considered as well as the sensitivity for the oligonucleotide design problem. However, a measure of evaluating the seeds regarding how adequate and efficient they are in the oligo design is not yet proposed. Here, we propose novel measures of evaluating the seeding algorithms based on the discriminability and the efficiency.

Results

To evaluate the proposed measures, we examine five seeding

SUBMITTER: Chung WH 

PROVIDER: S-EPMC2788383 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature