Computational identification of putative programmedtranslational frameshift sites
Identifieur interne : 003404 ( Main/Exploration ); précédent : 003403; suivant : 003405Computational identification of putative programmedtranslational frameshift sites
Auteurs : Atul A. Shah [États-Unis] ; Michael C. Giddings [États-Unis] ; Jasmin B. Parvaz [États-Unis] ; Raymond F. Gesteland [États-Unis] ; John F. Atkins [États-Unis] ; Ivaylo P. Ivanov [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2002.
Abstract
Motivation: In an effort to identify potential programmed frameshift sites by statistical analysis, we explore the hypothesis that selective pressure would have rendered such sites underabundant and underrepresented in protein-coding sequences. We developed a computer program to compare the frequencies of k-length subsequences of nucleotides with the frequencies predicted by a zero order Markov chain determined by the codon bias of the same set of sequences. The program was used to calculate and evaluate the distribution of 7-base oligonucleotides in the 6000+ putative protein-coding sequences of S. cerevisiae preliminary to the laboratory testing of the most highly underrepresented oligos for frameshifting efficiency. Results: Among the most significant results is the finding that the heptanucleotides CUU-AGG-C and CUU-AGU-U, sites of the programmed +1 translational frameshifts required for the production in yeast of actin filament-binding protein ABP140 and telomerase subunit EST3, respectively, rank among the least represented of phase I heptanucleotides in the coding sequences of S. cerevisiae. Laboratory experiments demonstrated that other underrepresented heptanucleotides identified by the program, for example GGU-CAG-A, are also prone to significant translational frameshifting, suggesting the possibility that genes containing other underrepresented heptamers may also encode transframe products. Availability: The program is available for download from http://www.gesteland.genetics.utah.edu/freqAnalysis Contact: ivaylo.ivanov@m.cc.utah.edu Supplementary Information: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis * To whom correspondence should be addressed. 2 Present address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Url:
DOI: 10.1093/bioinformatics/18.8.1046
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000D81
- to stream Istex, to step Curation: 000D81
- to stream Istex, to step Checkpoint: 000D63
- to stream Main, to step Merge: 003440
- to stream Main, to step Curation: 003404
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Computational identification of putative programmedtranslational frameshift sites</title><author><name sortKey="Shah, Atul A" sort="Shah, Atul A" uniqKey="Shah A" first="Atul A." last="Shah">Atul A. Shah</name></author><author><name sortKey="Giddings, Michael C" sort="Giddings, Michael C" uniqKey="Giddings M" first="Michael C." last="Giddings">Michael C. Giddings</name></author><author><name sortKey="Parvaz, Jasmin B" sort="Parvaz, Jasmin B" uniqKey="Parvaz J" first="Jasmin B." last="Parvaz">Jasmin B. Parvaz</name></author><author><name sortKey="Gesteland, Raymond F" sort="Gesteland, Raymond F" uniqKey="Gesteland R" first="Raymond F." last="Gesteland">Raymond F. Gesteland</name></author><author><name sortKey="Atkins, John F" sort="Atkins, John F" uniqKey="Atkins J" first="John F." last="Atkins">John F. Atkins</name></author><author><name sortKey="Ivanov, Ivaylo P" sort="Ivanov, Ivaylo P" uniqKey="Ivanov I" first="Ivaylo P." last="Ivanov">Ivaylo P. Ivanov</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:43645840A850BBA0296890E842C11632D3C79256</idno><date when="2002" year="2002">2002</date><idno type="doi">10.1093/bioinformatics/18.8.1046</idno><idno type="url">https://api.istex.fr/ark:/67375/HXZ-VRWQJ8X4-Z/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000D81</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000D81</idno><idno type="wicri:Area/Istex/Curation">000D81</idno><idno type="wicri:Area/Istex/Checkpoint">000D63</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000D63</idno><idno type="wicri:doubleKey">1367-4803:2002:Shah A:computational:identification:of</idno><idno type="wicri:Area/Main/Merge">003440</idno><idno type="wicri:Area/Main/Curation">003404</idno><idno type="wicri:Area/Main/Exploration">003404</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Computational identification of putative programmed
translational frameshift sites</title><author><name sortKey="Shah, Atul A" sort="Shah, Atul A" uniqKey="Shah A" first="Atul A." last="Shah">Atul A. Shah</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author><author><name sortKey="Giddings, Michael C" sort="Giddings, Michael C" uniqKey="Giddings M" first="Michael C." last="Giddings">Michael C. Giddings</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author><author><name sortKey="Parvaz, Jasmin B" sort="Parvaz, Jasmin B" uniqKey="Parvaz J" first="Jasmin B." last="Parvaz">Jasmin B. Parvaz</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author><author><name sortKey="Gesteland, Raymond F" sort="Gesteland, Raymond F" uniqKey="Gesteland R" first="Raymond F." last="Gesteland">Raymond F. Gesteland</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author><author><name sortKey="Atkins, John F" sort="Atkins, John F" uniqKey="Atkins J" first="John F." last="Atkins">John F. Atkins</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author><author><name sortKey="Ivanov, Ivaylo P" sort="Ivanov, Ivaylo P" uniqKey="Ivanov I" first="Ivaylo P." last="Ivanov">Ivaylo P. Ivanov</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Human Genetics, University of Utah, SLC, UT 84112-5330</wicri:regionArea><wicri:noRegion>UT 84112-5330</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="published">2002</date><biblScope unit="vol">18</biblScope><biblScope unit="issue">8</biblScope><biblScope unit="page" from="1046">1046</biblScope><biblScope unit="page" to="1053">1053</biblScope></imprint><idno type="ISSN">1367-4803</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: In an effort to identify potential programmed frameshift sites by statistical analysis, we explore the hypothesis that selective pressure would have rendered such sites underabundant and underrepresented in protein-coding sequences. We developed a computer program to compare the frequencies of k-length subsequences of nucleotides with the frequencies predicted by a zero order Markov chain determined by the codon bias of the same set of sequences. The program was used to calculate and evaluate the distribution of 7-base oligonucleotides in the 6000+ putative protein-coding sequences of S. cerevisiae preliminary to the laboratory testing of the most highly underrepresented oligos for frameshifting efficiency. Results: Among the most significant results is the finding that the heptanucleotides CUU-AGG-C and CUU-AGU-U, sites of the programmed +1 translational frameshifts required for the production in yeast of actin filament-binding protein ABP140 and telomerase subunit EST3, respectively, rank among the least represented of phase I heptanucleotides in the coding sequences of S. cerevisiae. Laboratory experiments demonstrated that other underrepresented heptanucleotides identified by the program, for example GGU-CAG-A, are also prone to significant translational frameshifting, suggesting the possibility that genes containing other underrepresented heptamers may also encode transframe products. Availability: The program is available for download from http://www.gesteland.genetics.utah.edu/freqAnalysis Contact: ivaylo.ivanov@m.cc.utah.edu Supplementary Information: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis * To whom correspondence should be addressed. 2 Present address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Shah, Atul A" sort="Shah, Atul A" uniqKey="Shah A" first="Atul A." last="Shah">Atul A. Shah</name></noRegion><name sortKey="Atkins, John F" sort="Atkins, John F" uniqKey="Atkins J" first="John F." last="Atkins">John F. Atkins</name><name sortKey="Gesteland, Raymond F" sort="Gesteland, Raymond F" uniqKey="Gesteland R" first="Raymond F." last="Gesteland">Raymond F. Gesteland</name><name sortKey="Giddings, Michael C" sort="Giddings, Michael C" uniqKey="Giddings M" first="Michael C." last="Giddings">Michael C. Giddings</name><name sortKey="Ivanov, Ivaylo P" sort="Ivanov, Ivaylo P" uniqKey="Ivanov I" first="Ivaylo P." last="Ivanov">Ivaylo P. Ivanov</name><name sortKey="Parvaz, Jasmin B" sort="Parvaz, Jasmin B" uniqKey="Parvaz J" first="Jasmin B." last="Parvaz">Jasmin B. Parvaz</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003404 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003404 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:43645840A850BBA0296890E842C11632D3C79256
|texte= Computational identification of putative programmedtranslational frameshift sites
}}
| This area was generated with Dilib version V0.6.33. |  |