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Efficient computation of spaced seed hashing with block indexing.
BMC Bioinformatics ; 19(Suppl 15): 441, 2018 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-30497364


Spaced-seeds, i.e. patterns in which some fixed positions are allowed to be wild-cards, play a crucial role in several bioinformatics applications involving substrings counting and indexing, by often providing better sensitivity with respect to k-mers based approaches. K-mers based approaches are usually fast, being based on efficient hashing and indexing that exploits the large overlap between consecutive k-mers. Spaced-seeds hashing is not as straightforward, and it is usually computed from scratch for each position in the input sequence. Recently, the FSH (Fast Spaced seed Hashing) approach was proposed to improve the time required for computation of the spaced seed hashing of DNA sequences with a speed-up of about 1.5 with respect to standard hashing computation.


In this work we propose a novel algorithm, Fast Indexing for Spaced seed Hashing (FISH), based on the indexing of small blocks that can be combined to obtain the hashing of spaced-seeds of any length. The method exploits the fast computation of the hashing of runs of consecutive 1 in the spaced seeds, that basically correspond to k-mer of the length of the run.


We run several experiments, on NGS data from simulated and synthetic metagenomic experiments, to assess the time required for the computation of the hashing for each position in each read with respect to several spaced seeds. In our experiments, FISH can compute the hashing values of spaced seeds with a speedup, with respect to the traditional approach, between 1.9x to 6.03x, depending on the structure of the spaced seeds.





Texto completo: Disponível Coleções: Bases de dados internacionais Base de dados: MEDLINE Assunto principal: Algoritmos / Biologia Computacional Idioma: Inglês Revista: BMC Bioinformatics Assunto da revista: Informática Médica Ano de publicação: 2018 Tipo de documento: Artigo País de afiliação: Itália