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Bioinformatics Advance Access published online on January 18, 2007
Bioinformatics, 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 a and Christopher J Lee b,*

aDepartment of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA. E-mail: shuriko{at}ucla.edu
bMolecular 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. E-mail: leec{at}mbi.ucla.edu

*To whom correspondence should be addressed. Christopher J Lee, E-mail: leec{at}chem.ucla.edu


  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 mult-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 data-base sizes and query interval widths. We also present an in-place NCList construction algorithm that yields database construction times that are approximately 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

Associate Editor: Golan Yona

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

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