—The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially ...
Matching regular expressions (regexps) is a very common workload. For example, tokenization, which consists of recognizing words or keywords in a character stream, appears in ever...
One of the most important collective communication patterns used in scientific applications is the complete exchange, also called All-to-All. Although efficient algorithms have b...
Background: The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest ap...
We analyse and compare the complexity of several algorithms for computing modular polynomials. We show that an algorithm relying on floating point evaluation of modular functions...