TY - JOUR
T1 - HyperPack
T2 - A software package for the study of levels, contexts, and patterns of APOBEC-mediated hypermutation in HIV
AU - Kijak, Gustavo H.
AU - Janini, Mario
AU - Tovanabutra, Sodsai
AU - Sanders-Buell, Eric E.
AU - Birx, Debora L.
AU - Robb, Merlin L.
AU - Michael, Nelson L.
AU - McCutchan, Francine E.
PY - 2007/4
Y1 - 2007/4
N2 - G-to-A hypermutation, a massive substitution of G for A, was first observed in HIV genomes 15 years ago. Initially ascribed to fluctuating nucleoutide pools or PCR errors, it has now been recognized as the result of an important host-defense mechanism mediated by APOBECs, a family of sequence-specific cytidine deaminases. Levels of hypermutation vary, and APOBECs have different preferences for the sequence contest of cytidines targeted for deamination; analysis of hypermutation provides important information about the host-virus interaction during viral replication. Here we present HyperPack, a software package to support systematic characterization of hypermutated sequences. Users can define the context of substitution for independent study of the effects of different APOBECs. The SubstrateScan and HyperScan modules are overlapping sliding-window strategies to analyze the distribution of targeted motifs and their substitution levels, respectively, across the viral genome. HyperPack is a platform-flexible, Java stand-alone application available through http://www.hivresearch.org/hyperpack/.
AB - G-to-A hypermutation, a massive substitution of G for A, was first observed in HIV genomes 15 years ago. Initially ascribed to fluctuating nucleoutide pools or PCR errors, it has now been recognized as the result of an important host-defense mechanism mediated by APOBECs, a family of sequence-specific cytidine deaminases. Levels of hypermutation vary, and APOBECs have different preferences for the sequence contest of cytidines targeted for deamination; analysis of hypermutation provides important information about the host-virus interaction during viral replication. Here we present HyperPack, a software package to support systematic characterization of hypermutated sequences. Users can define the context of substitution for independent study of the effects of different APOBECs. The SubstrateScan and HyperScan modules are overlapping sliding-window strategies to analyze the distribution of targeted motifs and their substitution levels, respectively, across the viral genome. HyperPack is a platform-flexible, Java stand-alone application available through http://www.hivresearch.org/hyperpack/.
UR - http://www.scopus.com/inward/record.url?scp=34247857484&partnerID=8YFLogxK
U2 - 10.1089/aid.2006.0279
DO - 10.1089/aid.2006.0279
M3 - Article
C2 - 17451344
AN - SCOPUS:34247857484
SN - 0889-2229
VL - 23
SP - 554
EP - 557
JO - AIDS Research and Human Retroviruses
JF - AIDS Research and Human Retroviruses
IS - 4
ER -