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Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes.
Artigo em Inglês | MEDLINE | ID: mdl-26356018
ABSTRACT
Information theory has been used for quite some time in the area of computational biology. In this paper we present a pattern discovery method, named Fast Entropic Profiler, that is based on a local entropy function that captures the importance of a region with respect to the whole genome. The local entropy function has been introduced by Vinga and Almeida in , here we discuss and improve the original formulation. We provide a linear time and linear space algorithm called Fast Entropic Profiler ( FastEP), as opposed to the original quadratic implementation. Moreover we propose an alternative normalization that can be also efficiently implemented. We show that FastEP is suitable for large genomes and for the discovery of patterns with unbounded length. FastEP is available at http://www.dei.unipd.it/~ciompin/main/FastEP.html.
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Texto completo: Disponível Coleções: Bases de dados internacionais Base de dados: MEDLINE Assunto principal: Reconhecimento Automatizado de Padrão / Genoma / Biologia Computacional / Teoria da Informação Idioma: Inglês Revista: ACM Trans Comput Biol Bioinform Assunto da revista: Biologia / Informática Médica Ano de publicação: 2014 Tipo de documento: Artigo