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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Published in:	PloS one Vol. 10; no. 7; p. e0132460
Main Authors:	Alves, Fernando, Cogo, Vinicius, Wandelt, Sebastian, Leser, Ulf, Bessani, Alysson
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 06.07.2015 Public Library of Science (PLoS)
Subjects:	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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Abstract	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.
AbstractList	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.
Audience	Academic
Author	Cogo, Vinicius Wandelt, Sebastian Leser, Ulf Bessani, Alysson Alves, Fernando
AuthorAffiliation	1 LaSIGE, University of Lisbon, Lisbon, Portugal Centro de Investigación y de Estudios Avanzados del IPN, MEXICO 2 WBI, Humboldt-Universität zu Berlin, Berlin, Germany
AuthorAffiliation_xml	– name: 1 LaSIGE, University of Lisbon, Lisbon, Portugal – name: Centro de Investigación y de Estudios Avanzados del IPN, MEXICO – name: 2 WBI, Humboldt-Universität zu Berlin, Berlin, Germany
Author_xml	– sequence: 1 givenname: Fernando surname: Alves fullname: Alves, Fernando – sequence: 2 givenname: Vinicius surname: Cogo fullname: Cogo, Vinicius – sequence: 3 givenname: Sebastian surname: Wandelt fullname: Wandelt, Sebastian – sequence: 4 givenname: Ulf surname: Leser fullname: Leser, Ulf – sequence: 5 givenname: Alysson surname: Bessani fullname: Bessani, Alysson
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/26146838$$D View this record in MEDLINE/PubMed
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CitedBy_id	crossref_primary_10_1186_s12859_022_04825_5 crossref_primary_10_1186_s12859_018_2230_2 crossref_primary_10_1002_cpe_6339 crossref_primary_10_1109_TC_2020_2994774 crossref_primary_10_1371_journal_pone_0232942
Cites_doi	10.1186/1748-7188-7-30 10.1186/1748-7188-8-25 10.1109/TCBB.2013.122 10.1126/science.1197891 10.1145/792548.611988 10.1016/0306-4573(94)90014-0 10.1093/bioinformatics/btn582 10.1038/ng.877 10.1093/bioinformatics/btr505 10.1186/1471-2164-9-517 10.1371/journal.pone.0109384 10.1093/hmg/ddq416 10.1093/bioinformatics/btp319
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 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.
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Title	On-Demand Indexing for Referential Compression of DNA Sequences
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