Rapid Homology Search with Neighbor Seeds
نویسندگان
چکیده
منابع مشابه
Rapid Homology Search with Two-Stage Extension and Daughter Seeds
Using a seed to rapidly “hit” possible homologies for further examination is a common practice to speed up homology search in molecular sequences. It has been shown that a collection of higher weight seeds have better sensitivity than a single lower weight seed at the same speed. However, huge memory requirements diminish the advantages of high weight seeds. This paper describes a twostage exte...
متن کاملIndel seeds for homology search
We are interested in detecting homologous genomic DNA sequences with the goal of locating approximate inverted, interspersed, and tandem repeats. Standard search techniques start by detecting small matching parts, called seeds, between a query sequence and database sequences. Contiguous seed models have existed for many years. Recently, spaced seeds were shown to be more sensitive than contiguo...
متن کاملOptimizing Multiple Spaced Seeds for Homology Search
Optimized spaced seeds improve sensitivity and specificity in local homology search. Several authors have shown that multiple seeds can have better sensitivity and specificity than single seeds. We describe a linear programming (LP)-based algorithm to optimize a set of seeds. Theoretically, our algorithm offers a performance guarantee: the sensitivity of a chosen seed set is at least 70% of wha...
متن کاملMultiple spaced seeds for homology search
MOTIVATION Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, Smi...
متن کاملQuick, Practical Selection of Effective Seeds for Homology Search
It has been observed that in homology search gapped seeds have better sensitivity than ungapped ones for the same cost (weight). In this paper, we propose a probability leakage model (a dissipative Markov system) to elucidate the mechanism that confers power to spaced seeds. Based on this model, we identify desirable features of gapped search seeds and formulate an extremely efficient procedure...
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ژورنال
عنوان ژورنال: Algorithmica
سال: 2007
ISSN: 0178-4617,1432-0541
DOI: 10.1007/s00453-007-0062-y