Table 1 Overview of computational tools.
From: Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C
Tool | Prediction method | Subtype |
|---|---|---|
T-CUP 2.0 | Uses structural information of the V3 loop by modelling the electrostatic potential and hydrophobicity; combination of results by stacking | subtype B (primarily) and C with 1351 sequences (200X4 and 1151 R5) |
Geno2pheno[coreceptor] | Support vector machine for binary classification | subtype B with 1100 sequences (769 R5, 210X4, 131 R5X4) from 332 patients |
PhenoSeq | Evaluation of HIV-1 V3 amino acid length, net amino acid charge, number of N-linked glycosylation sites and the frequency of site-specific amino acid alterations | A, A1, A2, B, C, D, CRF_01_AE, CRF02_AG |
WebPSSM x4r5 | Scoring matrices, reflecting the difference in abundance of a particular amino acid at a particular site | subtype B |
WebPSSM sinsi | Scoring matrices, reflecting the difference in abundance of a particular amino acid at a particular site | subtype B |
WebPSSM sinsiC | Scoring matrices, reflecting the difference in abundance of a particular amino acid at a particular site | subtype C |
Genotypic rule (Raymond et al.) | 11/25 rule in combination with a net charge rule | subtype C |
Genotypic rule (Esbjörnsson et al.) | Rules based on Raymond et al. with modified cut-offs of the mean net charge and total count of charged amino acids | subtype A |
