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Genome-wide selection of unique and valid oligonucleotides.

Hyyrö, Heikki; Juhola, Martti and Vihinen, Mauno LU (2005) In Nucleic Acids Research 33(13). p.115-115
Abstract
Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other... (More)
Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Amino Acids: analysis, Genomics: methods, Nucleotides: analysis, Oligonucleotide Probes: chemistry, Proteins: chemistry
in
Nucleic Acids Research
volume
33
issue
13
pages
115 - 115
publisher
Oxford University Press
external identifiers
  • pmid:16049019
  • scopus:27144468325
ISSN
1362-4962
DOI
10.1093/nar/gni110
language
English
LU publication?
no
id
5694b57d-b9ff-4467-a0a5-537d9ea45213 (old id 3635409)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/16049019?dopt=Abstract
date added to LUP
2013-06-12 16:13:37
date last changed
2017-01-01 07:39:13
@article{5694b57d-b9ff-4467-a0a5-537d9ea45213,
  abstract     = {Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied.},
  author       = {Hyyrö, Heikki and Juhola, Martti and Vihinen, Mauno},
  issn         = {1362-4962},
  keyword      = {Amino Acids: analysis,Genomics: methods,Nucleotides: analysis,Oligonucleotide Probes: chemistry,Proteins: chemistry},
  language     = {eng},
  number       = {13},
  pages        = {115--115},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Genome-wide selection of unique and valid oligonucleotides.},
  url          = {http://dx.doi.org/10.1093/nar/gni110},
  volume       = {33},
  year         = {2005},
}