%0 Journal Article
%T Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds
%A Laurent No¨¦
%J Archive of "Algorithms for Molecular Biology : AMB".
%D 2017
%R 10.1186/s13015-017-0092-1
%X Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of arbitrary chosen parameters from the probabilistic alignment models used. In this general context, Dominant seeds have been introduced by Mak and Benson (Bioinformatics 25:302¨C308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a parameter-free calculation of the sensitivity
%K Spaced seeds
%K Dominant seeds
%K Bernoulli
%K Hit Integration
%K Heaviside
%K Dirac
%K Counting semi-ring
%K Polynomial form
%K DFA
%U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5310094/