SPINE: Putting Backbone into String Indexing

The indexing technique commonly used for long strings, such as genomes, is the suffix tree, which is based on a vertical (intra-path) compaction of the underlying trie structure. In this paper, we investigate 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 string, 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 strings s...

• Type: Conference
• Year: 2004
• Where: ICDE
• Authors: Naresh Neelapala, Romil Mittal, Jayant R. Haritsa
• Keywords: Database, Horizontally-compacted Trie Index, ICDE 2004, SPINE Construction, Trie Structure