Computational identification of putative programmedtranslational frameshift sites
Identifieur interne : 000D81 ( Istex/Corpus ); précédent : 000D80; suivant : 000D82Computational identification of putative programmedtranslational frameshift sites
Auteurs : Atul A. Shah ; Michael C. Giddings ; Jasmin B. Parvaz ; Raymond F. Gesteland ; John F. Atkins ; Ivaylo P. IvanovSource :
- 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
Links to Exploration step
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<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>
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<profileDesc><abstract xml:lang="en"><p>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 <hi rend="italic">S. cerevisiae</hi>
preliminary to the laboratory testing
of the most highly underrepresented oligos for frameshifting
efficiency.</p>
<p>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 <hi rend="italic">S. cerevisiae</hi>
. 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.</p>
<p>Availability: The program is available for download from
<ref type="url">http://www.gesteland.genetics.utah.edu/freqAnalysis</ref>
</p>
<p>Contact: <ref type="email">ivaylo.ivanov@m.cc.utah.edu</ref>
</p>
<p>Supplementary Information: Complete results from the
analysis of <hi rend="italic">S. cerevisiae</hi>
are available on
<ref type="url">http://www.gesteland.genetics.utah.edu/freqAnalysis</ref>
</p>
<p><note place="inline" n="FN0"><ref>*</ref>
<p>To whom correspondence should be addressed.</p>
</note>
</p>
<p><note place="inline" n="FN2"><ref>2</ref>
<p>Present address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.</p>
</note>
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<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-title>Bioinformatics</journal-title>
<abbrev-journal-title abbrev-type="publisher">Bioinformatics</abbrev-journal-title>
<issn pub-type="ppub">1367-4803</issn>
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<title-group><article-title>Computational identification of putative programmed
translational frameshift sites</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author"><name><surname>Shah</surname>
<given-names>Atul A.</given-names>
</name>
<xref rid="AFF1">1</xref>
<xref rid="FN2">2</xref>
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<contrib contrib-type="author"><name><surname>Giddings</surname>
<given-names>Michael C.</given-names>
</name>
<xref rid="AFF1">1</xref>
<xref rid="FN2">2</xref>
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<contrib contrib-type="author"><name><surname>Parvaz</surname>
<given-names>Jasmin B.</given-names>
</name>
<xref rid="AFF1">1</xref>
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<contrib contrib-type="author"><name><surname>Gesteland</surname>
<given-names>Raymond F.</given-names>
</name>
<xref rid="AFF1">1</xref>
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<contrib contrib-type="author"><name><surname>Atkins</surname>
<given-names>John F.</given-names>
</name>
<xref rid="AFF1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ivanov</surname>
<given-names>Ivaylo P.</given-names>
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<xref rid="AFF1">1</xref>
<xref rid="FN0">*</xref>
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<aff id="AFF1"><label>1</label>
Department of Human Genetics,
University of Utah, SLC, UT 84112-5330, USA
</aff>
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<pub-date pub-type="ppub"><month>8</month>
<year>2002</year>
</pub-date>
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<issue>8</issue>
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<lpage>1053</lpage>
<history><date date-type="accepted"><day>12</day>
<month>2</month>
<year>2002</year>
</date>
<date date-type="received"><day>9</day>
<month>8</month>
<year>2001</year>
</date>
<date date-type="rev-recd"><day>12</day>
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<year>2002</year>
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<permissions><copyright-statement>© Oxford University Press
2002</copyright-statement>
<copyright-year>2002</copyright-year>
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<abstract xml:lang="en">
<p>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 <italic>S. cerevisiae</italic>
preliminary to the laboratory testing
of the most highly underrepresented oligos for frameshifting
efficiency.</p>
<p>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 <italic>S. cerevisiae</italic>
. 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.</p>
<p>Availability: The program is available for download from
<ext-link xlink:href="http://www.gesteland.genetics.utah.edu/freqAnalysis" ext-link-type="url">http://www.gesteland.genetics.utah.edu/freqAnalysis</ext-link>
</p>
<p>Contact: <ext-link xlink:href="ivaylo.ivanov@m.cc.utah.edu" ext-link-type="email">ivaylo.ivanov@m.cc.utah.edu</ext-link>
</p>
<p>Supplementary Information: Complete results from the
analysis of <italic>S. cerevisiae</italic>
are available on
<ext-link xlink:href="http://www.gesteland.genetics.utah.edu/freqAnalysis" ext-link-type="url">http://www.gesteland.genetics.utah.edu/freqAnalysis</ext-link>
</p>
<p>
<fn id="FN0" xml:lang="en">
<label>*</label>
<p>To whom correspondence should be
addressed.</p>
</fn>
</p>
<p>
<fn id="FN2" xml:lang="en">
<label>2</label>
<p>Present address: Department of Microbiology and
Immunology, University of North Carolina at Chapel Hill, Chapel
Hill, NC 27599, USA.</p>
</fn>
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<name type="personal"><namePart type="given">Atul A.</namePart>
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<name type="personal"><namePart type="given">Raymond F.</namePart>
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<name type="personal"><namePart type="given">Ivaylo P.</namePart>
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<abstract 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.</abstract>
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