Full-text indexes provide fast substring search over large text collections. A serious problem
of these indexes has traditionally been their space consumption. A recent trend is to develop …

Background The use of novel algorithmic techniques is pivotal to many important problems
in life science. For example the sequencing of the human genome [1] would not have been …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …

The primary goal of this article is to survey state-of-the-art indexing methods for approximate
dictionary searching. To improve understanding of the field, we introduce a taxonomy that …

A compressed full-text self-index represents a text in a compressed form and still answers
queries efficiently. This represents a significant advancement over the (full-) text indexing …

Background Identifying the bacteria and viruses present in a complex sample is useful in
disease diagnostics, product safety, environmental characterization, and research. Array …

We present Masai, a read mapper representing the state-of-the-art in terms of speed and
accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times …

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 …

Sequence datasets are ubiquitous in modern life-science applications, and querying
sequences is a common and critical operation in many of these applications. The suffix tree …

With the exponential growth of biological sequence databases, it has become critical to
develop effective techniques for storing, querying, and analyzing these massive data. Suffix …