SpEED: fast computation of sensitive spaced seeds
Open Access
- 20 June 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 27 (17), 2433-2434
- https://doi.org/10.1093/bioinformatics/btr368
Abstract
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.Keywords
This publication has 11 references indexed in Scilit:
- SHRiMP2: Sensitive yet Practical Short Read MappingBioinformatics, 2011
- BFAST: An Alignment Tool for Large Scale Genome ResequencingPLOS ONE, 2009
- On the complexity of the spaced seedsJournal of Computer and System Sciences, 2007
- Multiple spaced seeds for homology searchBioinformatics, 2007
- A fast and flexible approach to oligonucleotide probe design for genomes and gene familiesBioinformatics, 2007
- A UNIFYING FRAMEWORK FOR SEED SENSITIVITY AND ITS APPLICATION TO SUBSET SEEDSJournal of Bioinformatics and Computational Biology, 2006
- Designing seeds for similarity search in genomic DNAJournal of Computer and System Sciences, 2005
- PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCHJournal of Bioinformatics and Computational Biology, 2004
- PatternHunter: faster and more sensitive homology searchBioinformatics, 2002
- Basic local alignment search toolJournal of Molecular Biology, 1990