DNA encoding for an efficient 'Omics processing

doi:10.1016/j.cmpb.2010.03.014

2010-11-01

PRE

Boštjan Murovec *

James M. Tiedje

Blaž Stres

DOI：10.1016/j.cmpb.2010.03.014

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摘要

En 中文

The exponential growth of available DNA sequences and the increased interoperability of biological information is triggering intergovernmental 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 achieved by encoding the nucleotides together with their trailing alignment 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 alignment information. The significance of the propositions is confirmed by the encouraging results from empirical tests. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Keyword:

DNA-64

NumFASTA

Binary DNA encoding

Binary nucleotide encoding

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期刊

Computer Methods and Programs in Biomedicine

IF:

4.8

论文数:

7.0K

被引数:

2.1W

机构

University of Ljubljana

学者数:

1.5W

论文数: 1.3W

被引数: 1.7W

michigan state university

学者数:

3.6W

论文数: 3.2W

被引数: 44

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