SpEED: fast computation of sensitive spaced seeds Journal Articles

abstract

• 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.

authors

• Ilie, Lucian
• Ilie, Silvana
• Mansouri Bigvand, Anahita

status

• published 

publication date

• September 1, 2011

has subject area

• 01 Mathematical Sciences (FoR)
• 06 Biological Sciences (FoR)
• 08 Information and Computing Sciences (FoR)
• Algorithms (MeSH)
• Bioinformatics (Science Metrix)
• Computational Biology (MeSH)
• Sequence Alignment (MeSH)
• Software (MeSH)

published in

• Bioinformatics  Journal

keywords

• Algorithms
• Computational Biology
• Sequence Alignment
• Software

Digital Object Identifier (DOI)

• 10.1093/bioinformatics/btr368

PubMed ID

• 21690104

start page

• 2433

end page

• 2434

volume

• 27

issue

• 17