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:
https://lup.lub.lu.se/record/3635454
- author
- Hyyrö, Heikki
; Juhola, Martti
and Vihinen, Mauno
LU
- publishing date
- 2005
- 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
- pmid:15567185
- 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
- 2016-04-04 08:56:51
- date last changed
- 2022-04-23 18:42:18
@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}},
keywords = {{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}},
doi = {{10.1016/j.compbiomed.2003.11.003}},
volume = {{35}},
year = {{2005}},
}