%0 Journal Article
%T FSH: fast spaced seed hashing exploiting adjacent hashes
%A Matteo Comin
%A Samuele Girotto
%J Archive of "Algorithms for Molecular Biology : AMB".
%D 2018
%R 10.1186/s13015-018-0125-4
%X Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as they can provide better sensitivity. Many of these applications require to compute the hashing of each position in the input sequences with respect to the given spaced seed, or to multiple spaced seeds. While the hashing of k-mers can be rapidly computed by exploiting the large overlap between consecutive k-mers, spaced seeds hashing is usually computed from scratch for each position in the input sequence, thus resulting in slower processing
%K Spaced seeds
%K K-mers
%K Efficient hashing
%U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863468/