Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved]
We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to ra...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2018-02-01
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| Series: | F1000Research |
| Subjects: | |
| Online Access: | https://f1000research.com/articles/6-1845/v2 |
| _version_ | 1811331411622232064 |
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| author | Dariya K. Sydykova Benjamin R. Jack Stephanie J. Spielman Claus O. Wilke |
| author_facet | Dariya K. Sydykova Benjamin R. Jack Stephanie J. Spielman Claus O. Wilke |
| author_sort | Dariya K. Sydykova |
| collection | DOAJ |
| description | We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend. |
| first_indexed | 2024-04-13T16:19:08Z |
| format | Article |
| id | doaj.art-a9e8997a153d444ab94e49429043d6c6 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-13T16:19:08Z |
| publishDate | 2018-02-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-a9e8997a153d444ab94e49429043d6c62022-12-22T02:39:58ZengF1000 Research LtdF1000Research2046-14022018-02-01610.12688/f1000research.12874.215080Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved]Dariya K. Sydykova0Benjamin R. Jack1Stephanie J. Spielman2Claus O. Wilke3Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USADepartment of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USAInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USADepartment of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USAWe describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend.https://f1000research.com/articles/6-1845/v2BioinformaticsProtein Chemistry & Proteomics |
| spellingShingle | Dariya K. Sydykova Benjamin R. Jack Stephanie J. Spielman Claus O. Wilke Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] F1000Research Bioinformatics Protein Chemistry & Proteomics |
| title | Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] |
| title_full | Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] |
| title_fullStr | Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] |
| title_full_unstemmed | Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] |
| title_short | Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved] |
| title_sort | measuring evolutionary rates of proteins in a structural context version 2 referees 4 approved |
| topic | Bioinformatics Protein Chemistry & Proteomics |
| url | https://f1000research.com/articles/6-1845/v2 |
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