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 The sequence is analyzed for contamination using BLAST with both public (GenBank) and personal (unpublished sequences) sequence databases.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.

Enter here your input sequence data as FASTA format

Test contamination?

A) Public HIV-1 GenBank Yes No.
Note: Blasting complete GenBank 199,106 sequences (Oct 2007) takes time and it is only useful for testing contamination of non-published sequences.

B) BLAST your private sequences for intra laboratory contamination.

Tool Information?

submit sequences
example sequences
tutorial
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.