Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney; Aaron Steele; Rory Carmichael; Anabel Rodriguez; Alicia T. Specht; Kim Ngo; Jun Li; Scott Emrich; Patricia L. Clark

doi:10.1371/journal.pcbi.1005531

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Open Access

Peer-reviewed

Research Article

Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney,

Current address: Siemens Healthineers, Elkhart, Indiana, United States of America

Affiliation Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America

http://orcid.org/0000-0001-5906-1025

⨯
Aaron Steele,

Affiliation Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
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Rory Carmichael,

Current address: Quantcast, San Francisco, California, United States of America

Affiliation Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
⨯
Anabel Rodriguez,

Affiliation Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
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Alicia T. Specht,

Affiliation Department of Applied and Computational Mathematics & Statistics, University of Notre Dame, Notre Dame, Indiana, United States of America
⨯
Kim Ngo,

Affiliations Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America, Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
⨯
Jun Li,

Affiliation Department of Applied and Computational Mathematics & Statistics, University of Notre Dame, Notre Dame, Indiana, United States of America

http://orcid.org/0000-0003-4353-5761

⨯
Scott Emrich ,

* E-mail: pclark1@nd.edu (PLC); semrich@nd.edu (SE)

Affiliation Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
⨯
Patricia L. Clark

* E-mail: pclark1@nd.edu (PLC); semrich@nd.edu (SE)

Affiliations Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America, Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America

http://orcid.org/0000-0001-5462-8248

⨯

Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney,
Aaron Steele,
Rory Carmichael,
Anabel Rodriguez,
Alicia T. Specht,
Kim Ngo,
Jun Li,
Scott Emrich,
Patricia L. Clark

Published: May 5, 2017
https://doi.org/10.1371/journal.pcbi.1005531

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Protein domains
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Sequence alignment
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Protein folding
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Gene ontologies
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Protein structure
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Protein structure comparison
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DNA-binding proteins
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