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 The sequence is analyzed for contamination using BLAST with both public (GenBank) and personal (unpublished sequences) sequence databases.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



HIV Quality Analysis Tool Classification Rules



Rule 1: FAIL = LOW QUALITY
Result assigned based on query sequence match with a HIV-1 sequence in the GenBank with >= 98% identical nucleotides.
 
Rule 2: FAIL = LOW QUALITY
Result assigned based on query sequence with two (2) or more frame deletion/insertion mutations. Query sequence match a HIV-1 sequence in the GenBank with < 98% identical nucleotides.

Rule 3: FAIL = LOW QUALITY
Result assigned based on query sequence with two (2) or more stop codons mutations and with less than two (2) frame shit mutations. Query sequence match a HIV-1 sequence in the GenBank with < 98% identical nucleotides.

Rule 4: PASS = HIGH QUALITY
Result assigned based on query sequence with less than two (2) stop codons and frame shift mutations. Query sequence match a HIV-1 sequence in the GenBank with < 98% identical nucleotides.



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.