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


BACKGROUND
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.
Kondrashov
Alexey S
AS
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. kondrash@umich.edu
Assis
Raquel
R
D000465:Algorithms; D001483:Base Sequence; D023281:Genomics / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software