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Nucleic Acids Research Advance Access originally published online on November 15, 2006
Nucleic Acids Research 2007 35(Database issue):D371-D375; doi:10.1093/nar/gkl855
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Nucleic Acids Research, 2007, Vol. 35, Database issue D371-D375
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

The HIV positive selection mutation database

Calvin Pan1, Joseph Kim, Lamei Chen2, Qi Wang1 and Christopher Lee1,2,*

Center for Computational Biology, University of California Los Angeles, CA, USA 1 Molecular Biology Institute, Institute for Genomics and Proteomics, University of California Los Angeles, CA, USA 2 Department of Chemistry and Biochemistry, University of California Los Angeles, CA, USA

*To whom correspondence should be addressed. Tel: +1 310 825 7374; Fax: +1 310 206 7286; Email: leec{at}chem.ucla.edu

Received August 16, 2006. Revised October 9, 2006. Accepted October 10, 2006.

The HIV positive selection mutation database is a large-scale database available at http://www.bioinformatics.ucla.edu/HIV/ that provides detailed selection pressure maps of HIV protease and reverse transcriptase, both of which are molecular targets of antiretroviral therapy. This database makes available for the first time a very large HIV sequence dataset (sequences from ~50 000 clinical AIDS samples, generously contributed by Specialty Laboratories, Inc.), which makes possible high-resolution selection pressure mapping. It provides information about not only the selection pressure on individual sites but also how selection pressure at one site is affected by mutations on other sites. It also includes datasets from other public databases, namely the Stanford HIV database [S. Y. Rhee, M. J. Gonzales, R. Kantor, B. J. Betts, J. Ravela and R. W. Shafer (2003) Nucleic Acids Res., 31, 298–303]. Comparison between these datasets in the database enables cross-validation with independent datasets and also specific evaluation of the effect of drug treatment.


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