Bridges: a tool for identifying local similarities in long sequences.

Abstract

Bridges is a heuristic search tool that uses short word matches to rapidly identify local similarities between sequences. It consists of three stages: filtering input sequences, identifying local similarities and post-processing local similarities. As input sequence data are released from memory after the filtering stage, genome-scale datasets can be efficiently compared in a single run. Bridges also includes 20 parameters, which enable the user to dictate the sensitivity and specificity of a search. Bridges is implemented in the C programming language and can be run on all platforms. Source code and documentation are available at http://github.com/rassis/bridges.