Compressing DNA sequence databases with coil

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dc.contributor.authorWhite, W. Timothy J.
dc.contributor.authorHendy, Michael D.
dc.date.accessioned2010-11-23T03:35:31Z
dc.date.accessioned2016-03-06T22:26:12Z
dc.date.accessioned2016-09-07T13:57:51Z
dc.date.availableNO_RESTRICTIONen_US
dc.date.available2010-11-23T03:35:31Z
dc.date.available2016-03-06T22:26:12Z
dc.date.available2016-09-07T13:57:51Z
dc.date.issued2008-05-20
dc.description.abstractBackground: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.en_US
dc.identifier.citationWhite, W. T. J., & Hendy, M. D. (2008). Compressing DNA sequence databases with coil. Bmc Bioinformatics, 9. doi: 10.1186/1471-2105-9-242en_US
dc.identifier.harvestedMassey_Dark
dc.identifier.harvestedMassey_Dark
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10179/9717
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.relation.isbasedonBioMed Centralen_US
dc.relation.isformatofhttp://www.biomedcentral.com/1471-2105/9/242en_US
dc.subjectDNA sequenceen_US
dc.subjectDatabasesen_US
dc.subject.otherFields of Research::280000 Information, Computing and Communication Sciences::280300 Computer Softwareen_US
dc.titleCompressing DNA sequence databases with coilen_US
dc.typeJournal Articleen_US
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