SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

We present a bioinformatic web server (SWAKK) for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, acro...

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Detalles Bibliográficos
Autores principales: Liang, Han, Zhou, Weihua, Landweber, Laura F.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538794/
https://www.ncbi.nlm.nih.gov/pubmed/16845032
http://dx.doi.org/10.1093/nar/gkl272
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author Liang, Han
Zhou, Weihua
Landweber, Laura F.
author_facet Liang, Han
Zhou, Weihua
Landweber, Laura F.
author_sort Liang, Han
collection PubMed
description We present a bioinformatic web server (SWAKK) for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure. In addition, for comparison or when a reference structure is unavailable, the server can also perform a sliding window analysis on the primary sequence. The SWAKK web server is available at .
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spelling pubmed-15387942006-08-18 SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis Liang, Han Zhou, Weihua Landweber, Laura F. Nucleic Acids Res Article We present a bioinformatic web server (SWAKK) for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure. In addition, for comparison or when a reference structure is unavailable, the server can also perform a sliding window analysis on the primary sequence. The SWAKK web server is available at . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538794/ /pubmed/16845032 http://dx.doi.org/10.1093/nar/gkl272 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Liang, Han
Zhou, Weihua
Landweber, Laura F.
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title_full SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title_fullStr SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title_full_unstemmed SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title_short SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
title_sort swakk: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538794/
https://www.ncbi.nlm.nih.gov/pubmed/16845032
http://dx.doi.org/10.1093/nar/gkl272
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