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 a small HIV reference dataset and personal (private 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.

Enter here your input sequence data as FASTA format

Test contamination?

A) Test Contamination Yes No.
Note: We changed the GenBank option as this option took a long time to compute. Anyway, BLAST at NCBI can do this job better than us. At present, we test inter lab contamination agains a small HIV-1 reference dataset. We expect that this change will allow more researchers to use their own private databases for intra-laboratory contamination (or sample mix-up identification) as the analysis are now faster.

B) BLAST your private sequences for intra laboratory contamination.

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.