Journal Article

Fast computation of neighbor seeds

Lucian Ilie and Silvana Ilie

in Bioinformatics

Volume 25, issue 6, pages 822-823
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI:
Fast computation of neighbor seeds

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  • Bioinformatics and Computational Biology


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Motivation: Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for computing good neighbor seeds are very slow (exponential).

Results: We give a polynomial-time heuristic algorithm that computes better neighbor seeds than previous ones while being several orders of magnitude faster.


Journal Article.  1396 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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