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AuthorMurovec, Boštjan
Tiedje, James M.
Stres, Blaž
Title DNA encoding for an efficient 'Omics processing / Boštjan Murovec, James M. Tiedje, Blaž Stres
Type/contenttype of material article - component part
Publication date2010
Physical descriptionstr. 175-190
Uncontrolled subject headingsmolekularna genetika / DNK / sekvence / bioinformatika
SummaryThe exponential growth of available DNA sequences and the increased interoperability of biological information is triggering intergoivernmental efforts aimed at increasing the access, dissemination, and analysis of sequence data. Achieving the efficient storage and processing of DNA material is an important goal that parallels well with the foreseen coding standardization on the horizon. This paper proposes novel coding approaches, for both the dissemination and processing of sequences, where the speed of the DNA processing is shown to be boosted by exploring more than the normally utilized eight bits for encoding a single nucleotide. Further gains are achived by encoding the nucleotides together with their trailing alignament information as a single 64-bit data structure. the paper also proposes a slight modification to the established FASTA scheme in order to improve on its representation of alignament information. The significance of the proposition is confirmed by the encouraging results from empirical tests.
See publication: TI=Computer methods and programs in biomedicine ISSN: 0169-2607.- Vol. 100, no. 2 (2010), str. 175-190

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