On-Demand Indexing for Referential Compression of DNA Sequences

The decreasing costs of genome sequencing is creating a demand for scalable storage and processing tools and techniques to deal with the large amounts of generated data. Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evoluti...

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Vydáno v:PloS one Ročník 10; číslo 7; s. e0132460
Hlavní autoři: Alves, Fernando, Cogo, Vinicius, Wandelt, Sebastian, Leser, Ulf, Bessani, Alysson
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Public Library of Science 06.07.2015
Public Library of Science (PLoS)
Témata:
Algorithms
Bioinformatics
Biological evolution
Chromosomes
Compression
Computer science
Data compression
Data Compression - methods
Demand
Deoxyribonucleic acid
DNA
DNA sequencing
Gene sequencing
Genomes
Genomics
Genomics - methods
Humans
Indexing
Indexing (Content analysis)
Molecular biology
Nucleotide sequence
Ratios
Sequence Analysis, DNA - methods
Software
Storage
ISSN:1932-6203, 1932-6203
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Shrnutí:The decreasing costs of genome sequencing is creating a demand for scalable storage and processing tools and techniques to deal with the large amounts of generated data. Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times. The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence. In this paper, we propose a method for improving the performance of referential compression by removing the most costly phase of the process, the complete reference indexing. Our approach, called On-Demand Indexing (ODI) compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average), while achieving similar compression ratios.
Bibliografie:ObjectType-Article-1
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Conceived and designed the experiments: FA VC AB. Performed the experiments: FA VC. Analyzed the data: FA VC SW UL AB. Contributed reagents/materials/analysis tools: FA SW. Wrote the paper: FA VC SW UL AB.
Current address: LaSIGE, DI, FC/UL, Room C6.3.35, Campo Grande, 1749—016, Lisbon, Portugal
Competing Interests: The authors have declared that no competing interests exist.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0132460