Title

Seeds for Effective Oligonucleotide Design

Authors

Lucian Ilie, The University of Western Ontario
Silvana Ilie, Ryerson University
Shima Khoshraftar, The University of Western Ontario
Anahita Mansouri Bigvand, The University of Western Ontario

Document Type

Article

Publication Date

6-1-2011

Volume

12

Issue

280

Journal

BMC Genomics

URL with Digital Object Identifier

http://dx.doi.org/10.1186/1471-2164-12-280

Abstract

BACKGROUND: DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms.

RESULTS: We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.

CONCLUSIONS: Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.