This program will allow you to compare an HIV sequence to a GenBank
database of all published sequences and/or a user database of sequences
(e.g. sequences generated in the same laboratory or country). The
comparison between query sequences and databases is performed by BLAST.
The BLAST results are used to define the level of identity between the
query sequences and the database sequences. A cut off of 98% identity
is used to suggest that the query sequence is not unique and can be
caused by contamination in the laboratory with previous published or
local strains of HIV-1.
The query sequence is also compared with the complete genome and
proteins of the HXB2 reference sequence (RefSeq NC_001802.1,
AF033819.3). The comparison results are used to estimate the location
of the query sequence in the HXB2 genome map and to identify the
presence of nucleotide polymorphisms that cause frame shift and
generate stop codons in HIV-1 proteins.
Problems, questions and
suggestions please contact:
de Oliveira or
Lehvaslaiho, South African
National Bioinformatics Institute, University of Western Cape, South