Genes, information and sense: complexity and knowledge retrieval.
Information capacity of nucleotide sequences measures the unexpectedness of a continuation of a given string of nucleotides, thus having a sound relation to a variety of biological issues. A continuation is defined in a way maximizing the entropy of the ensemble of such continuations. The capacity is defined as a mutual entropy of real frequency dictionary of a sequence with respect to the one bearing the most expected continuations; it does not depend on the length of strings contained in a dictionary. Various genomes exhibit a multi-minima pattern of the dependence of information capacity on the string length, thus reflecting an order within a sequence. The strings with significant deviation of an expected frequency from the real one are the words of increased information value. Such words exhibit a non-random distribution alongside a sequence, thus making it possible to retrieve the correlation between a structure, and a function encoded within a sequence.
Sadovsky
Michael G
MG
Institute of Computational Modelling of RAS, Akademgorodok, 660036, Krasnoyarsk, Russia. msad@icm.krasn.ru
Putintseva
Julia A
JA
Shchepanovsky
Alexander S
AS
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D013329:Structure-Activity Relationship
D004247:DNA