Improved ESP-index: a practical self-index for highly repetitive texts

Abstract

While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing (ESP), an efficient parsing algorithm that guarantees upper bounds of parsing discrepancies between different appearances of the same subtexts in a text. Although ESP-index performs efficient top-down searches of query texts, it has a serious issue on binary searches for finding appearances of variables for a query text, which resulted in slowing down the query searches. We present an improved ESP-index (ESP-index-I) by leveraging the idea behind succinct data structures for large alphabets. While ESP-index-I keeps the same types of efficiencies as ESP-index about the top-down searches, it avoid the binary searches using fast rank/select operations. We experimentally test ESP-index-I on the ability to search query texts and extract subtexts from real world repetitive texts on a large-scale, and we show that ESP-index-I performs better that other possible approaches.Comment: This is the full version of a proceeding accepted to the 11th International Symposium on Experimental Algorithms (SEA2014