MersV1, Istex, Corpus, bibRecord, 000D81

Computational identification of putative programmedtranslational frameshift sites

Identifieur interne : 000D81 ( Istex/Corpus ); précédent : 000D80; suivant : 000D82

Computational identification of putative programmedtranslational frameshift sites

Auteurs : Atul A. Shah ; Michael C. Giddings ; Jasmin B. Parvaz ; Raymond F. Gesteland ; John F. Atkins ; Ivaylo P. Ivanov

Source :

Bioinformatics [ 1367-4803 ] ; 2002.

RBID : ISTEX:43645840A850BBA0296890E842C11632D3C79256

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:

https://api.istex.fr/ark:/67375/HXZ-VRWQJ8X4-Z/fulltext.pdf

DOI: 10.1093/bioinformatics/18.8.1046

Links to Exploration step

ISTEX:43645840A850BBA0296890E842C11632D3C79256

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<forename type="first">Ivaylo P.</forename>
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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="nlm-ta">Bioinformatics</journal-id>

<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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<article-categories><subj-group subj-group-type="heading"><subject>Original Paper</subject>
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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>

      </contrib>
<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>

      </contrib>
<contrib contrib-type="author"><name><surname>Parvaz</surname>
<given-names>Jasmin B.</given-names>
</name>

        

        

      

      <xref rid="AFF1">1</xref>

      </contrib>
<contrib contrib-type="author"><name><surname>Gesteland</surname>
<given-names>Raymond F.</given-names>
</name>

        

        

      

      <xref rid="AFF1">1</xref>

      </contrib>
<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>
</name>

        

        

      

      <xref rid="AFF1">1</xref>

      <xref rid="FN0">*</xref>

      

    </contrib>
<aff id="AFF1"><label>1</label>Department of Human Genetics,

   University of Utah, SLC, UT 84112-5330, USA

   </aff>
</contrib-group>
<pub-date pub-type="ppub"><month>8</month>
<year>2002</year>
</pub-date>
<volume>18</volume>
<issue>8</issue>
<fpage>1046</fpage>
<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>
<month>1</month>
<year>2002</year>
</date>
</history>
<permissions><copyright-statement>© Oxford University Press

 2002</copyright-statement>
<copyright-year>2002</copyright-year>
</permissions>
<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>

      </p>

    </abstract>
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<titleInfo type="alternative" lang="en" contentType="CDATA"><title>Computational identification of putative programmed translational frameshift sites</title>
</titleInfo>
<name type="personal"><namePart type="given">Atul A.</namePart>
<namePart type="family">Shah</namePart>
<affiliation>Department of Human Genetics, University of Utah, SLC, UT 84112-5330, USA</affiliation>
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<name type="personal"><namePart type="given">Michael C.</namePart>
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<name type="personal"><namePart type="given">Jasmin B.</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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Computational identification of putative programmedtranslational frameshift sites

Computational identification of putative programmedtranslational frameshift sites

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