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Title of Journal: Chin Sci Bull

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Abbravation: Chinese Science Bulletin

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SP Science China Press

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DOI

10.1006/cryo.1996.0032

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ISSN

1861-9541

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Overlap digraph An effective model for finding go

Authors: Ke Chen Kun She QingXin Zhu
Publish Date: 2011/04/26
Volume: 56, Issue: 11, Pages: 1100-
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Abstract

Spaced seeds technology which was proposed by PatternHunter has been proven to be more sensitive and faster than continuous seeds and it is now widely used for biosequence local alignments However finding optimal spaced seeds is an NPhard problem A seed digraph model is proposed to find good spaced seeds which are very close to optimal in a very different but effective way Using this different approach some good long spaced seeds which cannot be calculated by normal optimal sensitivity formulas due to their exponential complexity can be found

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