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.
Efficient computation of spaced seed hashing with block indexing
Girotto S.;Comin M.;Pizzi C.
2018
Abstract
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.Pubblicazioni consigliate
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