DNA encoding for an efficient 'Omics processing

Murovec, Boštjan (author), Tiedje, James M. (author), Stres, Blaž (author)

The 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.

• Language: English
• Keywords: molekularna genetika, DNK, sekvence, bioinformatika
• Work type: Not categorized
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Year: 2010
• Number of pages: Str. 175-190
• Numbering: Vol. 100, no. 2
• PID: 20.500.12556/RUL-36518
• UDC: 575
• ISSN on article: 0169-2607
• DOI: 10.1016/j.cmpb.2010.03.014
• COBISS.SI-ID: 2625416
• Publication date in RUL: 10.07.2015

Record is a part of a journal

• Title: Computer methods and programs in biomedicine
• Shortened title: Comput. methods programs biomed.
• Publisher: Elsevier
• ISSN: 0169-2607
• COBISS.SI-ID: 25260032