Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

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• 作者：Laurent Noé
• 关键词：Spaced seeds ; Dominant seeds ; Bernoulli ; Hit Integration ; Heaviside ; Dirac ; Counting semi ; ring ; Polynomial form ; DFA
• 刊名：Algorithms for Molecular Biology
• 出版年：2017
• 出版时间：December 2017
• 年：2017
• 卷：12
• 期：1
• 全文大小：2446KB
• 刊物主题：Bioinformatics; Computational Biology/Bioinformatics; Physiological, Cellular and Medical Topics; Algorithms;
• 出版者：BioMed Central
• ISSN：1748-7188
• 卷排序：12

文摘

BackgroundSpaced 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 25:302–308, 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.