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Bioinformatics Advance Access originally published online on November 7, 2008
Bioinformatics 2009 25(2):274-275; doi:10.1093/bioinformatics/btn582
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Human genomes as email attachments

Scott Christley 1,{dagger}, Yiming Lu 1,{dagger}, Chen Li 1,* and Xiaohui Xie 1,2,*

1Department of Computer Science and 2Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The amount of genomic sequence data being generated and made available through public databases continues to increase at an ever-expanding rate. Downloading, copying, sharing and manipulating these large datasets are becoming difficult and time consuming for researchers. We need to consider using advanced compression techniques as part of a standard data format for genomic data. The inherent structure of genome data allows for more efficient lossless compression than can be obtained through the use of generic compression programs. We apply a series of techniques to James Watson's genome that in combination reduce it to a mere 4MB, small enough to be sent as an email attachment.

Availability: Our algorithms are implemented in C++ and are freely available from http://www.ics.uci.edu/~xhx/project/DNAzip.

Contact: chenli{at}ics.uci.edu; xhx{at}ics.uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received on October 7, 2008; revised on October 31, 2008; accepted on November 6, 2008

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M. C. Brandon, D. C. Wallace, and P. Baldi
Data structures and compression algorithms for genomic sequence data
Bioinformatics, July 15, 2009; 25(14): 1731 - 1738.
[Abstract] [Full Text] [PDF]


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