Can I read Seeds for Effective Oligonucleotide Design on EtoBox?

Seeds for Effective Oligonucleotide Design by Lucian Ilie; Silvana Ilie; Shima Khoshraftar; Anahita Mansouri Bigvand is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Seeds for Effective Oligonucleotide Design about?

## 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.

Who reads Seeds for Effective Oligonucleotide Design?

Author

Lucian Ilie; Silvana Ilie; Shima Khoshraftar; Anahita Mansouri Bigvand

Publisher

BioMed Central; Springer (Biomed Central Ltd.); London: BioMed Central, 2000-; Springer Science and Business Media LLC; Society for Mining, Metallurgy and Exploration Inc. (ISSN 1471-2164)

Published

2011

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)