All hits all the time: parameter-free calculation of spaced seed sensitivity | Zendy

Denise Mak | Zendy; Gary Benson | Zendy

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All hits all the time: parameter-free calculation of spaced seed sensitivity

Author(s) -

Denise Mak,

Gary Benson

Publication year - 2008

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btn643

Subject(s) - indel , sensitivity (control systems) , computer science , preprocessor , probability distribution , selection (genetic algorithm) , set (abstract data type) , algorithm , matching (statistics) , random seed , mathematics , statistics , artificial intelligence , biology , genetics , pseudorandom number generator , electronic engineering , gene , genotype , single nucleotide polymorphism , engineering , programming language

Standard search techniques for DNA repeats start by identifying small matching words, or seeds, that may inhabit larger repeats. Recent innovations in seed structure include spaced seeds and indel seeds which are more sensitive than contiguous seeds. Evaluating seed sensitivity requires (i) specifying a homology model for alignments and (ii) assigning probabilities to those alignments. Optimal seed selection is resource intensive because all alternative seeds must be tested. Current methods require that the model and its probability parameters be specified in advance. When the parameters change, the entire calculation has to be rerun.

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