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Open Access Research article

Seeds for effective oligonucleotide design

Lucian Ilie1*, Silvana Ilie2, Shima Khoshraftar1 and Anahita Mansouri Bigvand1

Author Affiliations

1 Department of Computer Science, University of Western Ontario, N6A 5B7, London, ON, Canada

2 Department of Mathematics, Ryerson University, M5B 2K3, Toronto, ON, Canada

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BMC Genomics 2011, 12:280  doi:10.1186/1471-2164-12-280

Published: 1 June 2011



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.


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.


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