Speaker: Jayant Haritsa, SERC
Abstract:
Suffix trees, a popular indexing technique for biological sequences, are based on vertical (intra-path) compaction of the underlying trie structure. In this talk, we present an alternative approach to index building, based on horizontal (inter-path) compaction of the trie. In particular, we present SPINE, a carefully engineered horizontally-compacted trie index. SPINE consists of a backbone formed by a linear chain of nodes representing the underlying biological sequence, with the nodes connected by a rich set of edges for facilitating fast forward and backward traversals over the backbone during index construction and query search. A special feature of SPINE is that it collapses the trie into a linear structure, representing the logical extreme of horizontal compaction.
We describe algorithms for SPINE construction and for searching this index to find the occurrences of query patterns. Our experimental results on a variety of real genomic and proteomic sequences show that SPINE requires significantly less space than standard implementations of suffix trees. Further, SPINE takes lesser time for both construction and search as compared to suffix trees, especially when the index is disk-resident. Finally, the linearity of its structure makes it more amenable for integration with database engines.