Afficher la couverture 'Subset seed automaton | Kucherov, Gregory' en grand format
/5

0 avis

Subset seed automaton

Archive ouverte

Kucherov, Gregory | Noé, Laurent | Roytberg, Mihkail

Edité par CCSD -

International audience. We study the pattern matching automaton introduced in [KucherovNoeRoytbergJBCB06] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained by applying the Aho-Corasick construction. We study properties of this automaton andpresent an efficient implementation of the automaton construction. We also present some experimental results and show that this automaton can be successfully applied to more general situations.

Suggestions

Du même auteur

A unifying framework for seed sensitivity and its application to subset seeds.

Archive ouverte | Kucherov, Gregory | CCSD

International audience. We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem--a ...

Efficient seeding techniques for protein similarity search

Archive ouverte | Roytberg, Mihkail | CCSD

International audience. We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with opt...

Protein similarity search with subset seeds on a dedicated reconfigurable hardware

Archive ouverte | Peterlongo, Pierre | CCSD

International audience. Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple se...

Chargement des enrichissements...