PhenoSeq
A suite of subtype specific V3 sequence-based coreceptor usage prediction
algorithms for HIV-1 subtypes A, A1, A2, B, C, D, CRF01_AE and CRF02_AG.
HXB2 V3
(reference sequence)
:
Type of V3 sequence:
Amino acid (without ambiguity "X")
Nucleotide (IUPAC nomenclature)
Subtype:
Unknown*
A/A1/A2/CRF02_AG
CRF01_AE
B
C
D
* The PhenoSeq "unknown" subtype option is temporarily out of order. It will be up and running again soon. In the meantime, please use an alternative HIV subtyping tool (such as COMET;
http://comet.retrovirology.lu
/ or REGA;
http://www.bioafrica.net/rega-genotype/html/
) then select the appropriate PhenoSeq algorithm.
Please submit
unaligned
sequence(s) containing the V3 region
only
in
FASTA
format with a
unique
name for each sequence, e.g.
>seq_1
CTRPNNNTRKSIRIGPGRAFVTIGKIGNMRQAHC
Paste in FASTA formatted V3 sequences to analyse:
Or upload a FASTA file to analyse:
The PhenoSeq platform will align submitted sequence(s) to HXB2 using the
European Bioinformatics Institute
Multiple Sequence Alignment
tools website
(Larkin, M. A et al.,
Bioinformatics
(Oxford, England) 23 (21):2947-8).
Produced by Kieran Cashin and colleagues from the Gorry Laboratory.
kieran@burnet.edu.au
Relevant literature:
Cashin K, et al., (2013)
Retrovirology
10
:24
Jakobsen MR, et al., (2013)
PLoS ONE
8
(6): e65950
Cashin K, et al., (2013)
Retrovirology
10
:98
Cashin K, et al., (2014)
PLoS ONE
9
(10): e109771
Cashin K, et al., (2015)
Scientific Reports.
5
:8543