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Bioinformatics Advance Access originally published online on January 18, 2007
Bioinformatics 2007 23(11):1386-1393; doi:10.1093/bioinformatics/btl647
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases

Alexander V. Alekseyenko 1 and Christopher J. Lee 2,*

1Department of Biomathematics, David Geffen School of Medicine and 2Molecular Biology Institute, Center for Computational Biology, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1570, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The exponential growth of sequence databases poses a major challenge to bioinformatics tools for querying alignment and annotation databases. There is a pressing need for methods for finding overlapping sequence intervals that are highly scalable to database size, query interval size, result size and construction/updating of the interval database.

Results: We have developed a new interval database representation, the Nested Containment List (NCList), whose query time is O(n + log N), where N is the database size and n is the size of the result set. In all cases tested, this query algorithm is 5–500-fold faster than other indexing methods tested in this study, such as MySQL multi-column indexing, MySQL binning and R-Tree indexing. We provide performance comparisons both in simulated datasets and real-world genome alignment databases, across a wide range of database sizes and query interval widths. We also present an in-place NCList construction algorithm that yields database construction times that are ~100-fold faster than other methods available. The NCList data structure appears to provide a useful foundation for highly scalable interval database applications.

Availability: NCList data structure is part of Pygr, a bioinformatics graph database library, available at http://sourceforge.net/projects/pygr

Contact: leec{at}chem.ucla.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Golan Yona

Received on June 16, 2006; revised on December 9, 2006; accepted on December 18, 2006

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