HIV-1 Sequence Quality Analysis Tool

This tool is designed to use determine the quality of a specific HIV sequence. The sequence is analyzed for contamination using BLAST with both public (GenBank) and personal (unpublished sequences) sequence databases. Sequence translational problems (such as frame shift and stop codons mutations) are identified using complete genome and the proteome of the HIV-1 reference sequence HXB2.

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, GenBank/EMBL/DDBJ 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.

Tool Information?

submit sequences
example sequences
decision trees

Problems, questions and suggestions please contact:
Tulio de Oliveira or Heikki Lehvaslaiho
, South African National Bioinformatics Institute, University of Western Cape, South Africa.

Page last updated by Tulio de Oliveira.