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On exact string matching of unique oligonucleotides.

Hyyrö, Heikki; Juhola, Martti and Vihinen, Mauno LU (2005) In Computers in Biology and Medicine 35(2). p.173-181
Abstract
Unique, gene-specific oligonucleotides are used for many genetic investigations such as polymerase chain reaction, gene cloning, microarray technology and antisense DNA studies. It is a computationally demanding task to extract these oligonucleotides from DNA databases. We studied the problem from the point of view of the string matching problem. We implemented and tested several exact string matching algorithms and modified the implementations to be as effective as possible. Ten different implementations were tested on yeast genomic sequence data. The run times for the best algorithms were significantly improved compared to conventional approaches, while in principle, i.e. in respect of theoretical time complexity, these algorithms do not... (More)
Unique, gene-specific oligonucleotides are used for many genetic investigations such as polymerase chain reaction, gene cloning, microarray technology and antisense DNA studies. It is a computationally demanding task to extract these oligonucleotides from DNA databases. We studied the problem from the point of view of the string matching problem. We implemented and tested several exact string matching algorithms and modified the implementations to be as effective as possible. Ten different implementations were tested on yeast genomic sequence data. The run times for the best algorithms were significantly improved compared to conventional approaches, while in principle, i.e. in respect of theoretical time complexity, these algorithms do not actually differ essentially from each other. (Less)
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Saccharomyces cerevisiae: genetics, Fungal: analysis, DNA, Oligonucleotides: genetics, Sequence Alignment: methods
in
Computers in Biology and Medicine
volume
35
issue
2
pages
173 - 181
publisher
Elsevier
external identifiers
  • pmid:15567185
  • scopus:9644263964
ISSN
1879-0534
DOI
10.1016/j.compbiomed.2003.11.003
language
English
LU publication?
no
id
3cd13f86-0712-4742-a8e9-6f69e58215a4 (old id 3635454)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/15567185?dopt=Abstract
date added to LUP
2013-06-12 16:09:55
date last changed
2017-01-22 04:17:35
@article{3cd13f86-0712-4742-a8e9-6f69e58215a4,
  abstract     = {Unique, gene-specific oligonucleotides are used for many genetic investigations such as polymerase chain reaction, gene cloning, microarray technology and antisense DNA studies. It is a computationally demanding task to extract these oligonucleotides from DNA databases. We studied the problem from the point of view of the string matching problem. We implemented and tested several exact string matching algorithms and modified the implementations to be as effective as possible. Ten different implementations were tested on yeast genomic sequence data. The run times for the best algorithms were significantly improved compared to conventional approaches, while in principle, i.e. in respect of theoretical time complexity, these algorithms do not actually differ essentially from each other.},
  author       = {Hyyrö, Heikki and Juhola, Martti and Vihinen, Mauno},
  issn         = {1879-0534},
  keyword      = {Saccharomyces cerevisiae: genetics,Fungal: analysis,DNA,Oligonucleotides: genetics,Sequence Alignment: methods},
  language     = {eng},
  number       = {2},
  pages        = {173--181},
  publisher    = {Elsevier},
  series       = {Computers in Biology and Medicine},
  title        = {On exact string matching of unique oligonucleotides.},
  url          = {http://dx.doi.org/10.1016/j.compbiomed.2003.11.003},
  volume       = {35},
  year         = {2005},
}