A new method for indexing genomes using on-disk suffix trees

Authors:
Marina Barsky;Ulrike Stege;Alex Thomo;Chris Upton
Affiliations:
University of Victoria, Victoria, BC, Canada;University of Victoria, Victoria, BC, Canada;University of Victoria, Victoria, BC, Canada;University of Victoria, Victoria, BC, Canada
Venue:
Proceedings of the 17th ACM conference on Information and knowledge management
Year:
2008

Citing 19
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Abstract

We propose a new method to build persistent suffix trees for indexing the genomic data. Our algorithm DiGeST (Disk-Based Genomic Suffix Tree) improves significantly over previous work in reducing the random access to the input string and performing only two passes over disk data. DiGeST is based on the two-phase multi-way merge sort paradigm using a concise binary representation of the DNA alphabet. Furthermore, our method scales to larger genomic data than managed before.