HIVseq accepts user-submitted RT, protease, and integrase sequences or mutations. Translated sequences are compared to the consensus subtype B reference sequence and the differences are used as query parameters for interrogating the HIV Drug Resistance Database to determine the prevalence of each mutation in antiretroviral class naïve or experienced patients with viruses belonging to subtypes A, B, C, D, F, G, CRF01_AE, and CRF02_AG. A detailed description of the program output can be found in the Release Notes.
Sequences can be entered as plain text if just one sequence is entered. Sequences must be entered using the FASTA format if multiple sequences are entered. Sequences can be pasted in the text box or uploaded using the File Upload option. The upper limit is currently 1000 sequences containing 3000 nucleotides per sequence.
The program output will contain an HTML page with a navigation sidebar linking to the results for each sequence. Detailed descriptions of the HTML and spreadsheet output are explained in the Release Notes.