Optimizing Multiple Seeds for Protein Homology Search
نویسندگان
چکیده
منابع مشابه
Optimizing 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...
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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 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...
متن کاملAmino Acid Classification and Hash Seeds for Homology Search
Spaced seeds have been extensively studied in the homology search field. A spaced seed can be regarded as a very special type of hash function on k-mers, where two k-mers have the same hash value if and only if they are identical at the w (w < k) positions designated by the seed. Spaced seeds substantially increased the homology search sensitivity. It is then a natural question to ask whether t...
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ژورنال
عنوان ژورنال: IEEE/ACM Transactions on Computational Biology and Bioinformatics
سال: 2005
ISSN: 1545-5963
DOI: 10.1109/tcbb.2005.13