AcoSeeD: an ant colony optimization for finding optimal spaced seeds in biological sequence search
ANTS'12 Proceedings of the 8th international conference on Swarm Intelligence
Design and analysis of periodic multiple seeds
Theoretical Computer Science
| Hi-index | 3.84 |
Summary: Multiple spaced seeds represent the current state-of-the-art for similarity search in bioinformatics, with applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present SpEED, a software program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude faster and computes better seeds than the existing leading software programs. Availability: The source code of SpEED is freely available at www.csd.uwo.ca/~ilie/SpEED/ Contact: ilie@csd.uwo.ca Supplementary information:Supplementary data are available at Bioinformatics online.