The combination of incessant advances in sequencing technology producing large amounts
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …

Suffix trees are by far the most important data structure in stringology, with a myriad of
applications in fields like bioinformatics and information retrieval. Classical representations …

Let A be an array of n elements taken from a totally ordered set. We present a data structure
of size 3 n+ o (n) bits that allows us to answer the following queries on A in constant time …

Exact string matching is a problem that computer programmers face on a regular basis, and
full-text indexes like the suffix tree or the suffix array provide fast string search over large …

Inverted indexes are the most fundamental and widely used data structures in information
retrieval. For each unique word occurring in a document collection, the inverted index stores …

Searching for genes encoding microRNAs (miRNAs) is an important task in genome
analysis. Because the secondary structure of miRNA (but not the sequence) is highly …

Let A be a static array storing n elements from a totally ordered set. We present a data
structure of optimal size at most nlog2 (3+ 22)+ o (n) bits that allows us to answer the …

In sequence analysis it is often advantageous to build an index data structure for large texts,
as many tasks--for instance repeated pattern matching--can then be solved in optimal time …

The suffix tree is a very important data structure in string processing, but typical
implementations suffer from huge space consumption. In large-scale applications …

Background Suffix arrays and their variants are used widely for representing genomes in
search applications. Enhanced suffix arrays (ESAs) provide fast search speed, but require …