Experiences Using Logic Programming in Bioinformatics
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
An overview of the HDF5 technology suite and its applications
Proceedings of the EDBT/ICDT 2011 Workshop on Array Databases
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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@chem.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online.