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 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
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United States
Public Library of Science
06.07.2015
Public Library of Science (PLoS) |
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| 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. |
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| 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 |
| ContentType | Journal Article |
| Copyright | COPYRIGHT 2015 Public Library of Science 2015 Alves et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2015 Alves et al 2015 Alves et al |
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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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| SubjectTerms | 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 |
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| Title | On-Demand Indexing for Referential Compression of DNA Sequences |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/26146838 https://www.proquest.com/docview/1694517190 https://www.proquest.com/docview/1694963442 https://pubmed.ncbi.nlm.nih.gov/PMC4493149 https://doaj.org/article/9cd23135cb004464bce93e481224381b http://dx.doi.org/10.1371/journal.pone.0132460 |
| Volume | 10 |
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