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J. Virol., Aug 1996, 5720-5730, Vol 70, No. 8
GH Learn Jr, BT Korber, B Foley, BH Hahn, SM Wolinsky and JI Mullins
Human immunodeficiency virus type 1 (HIV-1) sequences are accumulating in
the literature at a rapid pace. For this ever-expanding resource to be
maximally useful, it is critical that researchers strive to maintain a high
level of quality assurance, both in experimental design and conduct and in
analyses. Here we present detailed analyses of problematic sets of HIV-1
sequences in the database that include sequence anomalies suggestive of
mislabeling or sample contamination problems. These data are examined in
the context of currently available HIV-1 sequence information to provide an
example of how to identify potentially flawed data. Indicators of potential
problems with sequences are (i) sequences that are nearly identical that
are supposed to be derived from unlinked individuals and that are markedly
distinct from other sequences from the putative source or (ii) sequences
that are nearly identical to those of laboratory strains. We provide an
outline of methods that researchers can use to perform preliminary
laboratory and computational analyses that could help identify problematic
data and thus help ensure the integrity of sequence databases.
Copyright © 1996, American Society for Microbiology
Maintaining the integrity of human immunodeficiency virus sequence databases
Department of Microbiology, University of Washington, Seattle 98195- 7740, USA.
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