HIV Databases HIV Databases home HIV Databases home
HIV sequence database



HIV Sequence Alignment and Related Data (VH and VL sequences, neutralization titers, clinical metadata) from Liao et al. 2013

Contents:

env.fasta
Alignment of 293 SGA env sequences from 703010505 (CH505), plus HXB2 and the Transmitted/Founder sequence. The second field indicates the sample timepoint (e.g., w4). The fourth field gives the GenBank accession number.

metadata.csv
Contains env sequence annotation as submitted to GenBank.

vh.fasta
Unaligned VH sequences. Sequences from mAbs have names like this:
703010505_CH103_KC575845 (id, mAb name, accession).
Sequences from pyrosequencing have names like this:
703010505_w53_10_29_KC575857 (id, timepoint, arbitrary sequence id, number of reads having this sequence, accession).

vl.fasta:
Unaligned VL sequences. Naming convention follows that in vh.fasta, though the multiplicity of 454 reads is 1.

ic50s.csv:
IC50 neutralization titers from monoclonal antibodies and inferred intermediates.

Click Here to download all files (.zip)

Reference:

Hua-Xin Liao, Rebecca Lynch, Tongqing Zhou, Feng Gao, S. Munir Alam, Scott D. Boyd, Andrew Z. Fire, Krishna M. Roskin, Chaim A. Schramm, Zhenhai Zhang, Jiang Zhu, Lawrence Shapiro, NISC Comparative Sequencing Program, James C. Mullikin, Gnana Gnanakaran, Peter Hraber, Kevin Weihe, Garnett Kelsoe, Guang Yang, Shi-Mao Xia, David C. Montefiori, Robert Parks, Krissey E. Lloyd, Richard M. Scearce, Kelly D. Soderberg, Myron Cohen, Gift Kaminga, Mark K Louder, Lillan M. Tran, Yue Chen, Fangping Cai, Sheri Chen, Stephanie Moquin, Xiulian Du, Gordon M. Joyce, Sanjay Srivatsan, Baoshan Zhang, Anqi Zheng, George M. Shaw, Beatrice H. Hahn, Thomas B. Kepler, Bette T.M. Korber, Peter D. Kwong, John R. Mascola, Barton F. Haynes.

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 497(7446):469-76, 2013. doi:10.1038/nature12053 PMID 23552890.

This study was supported by the National Institutes of Allergy and Infectious Diseases and by intramural NIH support for the NIAID Vaccine Research Center, by grants from the NIH, NIAID, AI067854 (The Center for HIV/AIDS Vaccine Immunology) and AI100645 (The Center for Vaccine Immunology-Immunogen Discovery).



last modified: Thu Dec 12 13:57 2013


Questions or comments? Contact us at seq-info@lanl.gov.

 
Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health