Coreceptor Usage Prediction Server

HIVcoPred: is a support Vectors Machine (SVM) and BLAST based prediction method for coreceptor used by HIV-1 from its thrid Hypervariable loop(V3). The Split Amino Acid Composition was generated and SVM score was claculated. BLAST E-value score generated for each submitted V3 loop and depending upon the E-value score, the Final SVM score was generated which was used for final prediction purpose.

Datasets
We used the following datasets in the development of HIVcoPRED:

CCR5 Sequences (N=1799)
CXCR4 Sequences (N=598)

The X4 dataset comprised 246 CXCR4-tropic and 352 R5X4-tropic V3 sequences, making a total of 598 sequences. The individual datasets sequences are given below:

CXCR4 Sequences (N=246)
R5X4 Sequences (N=352)

where 'N' is the number of V3 sequences in each dataset.

Independent Datasets
In this study, we used an independent dataset of 256 R5- and 81 X4-tropic sequences(R5-256 ; X4-81). This independent dataset was not included in the training set of our models.
The following datasets were used to make a robust independent dataset :
Wetcat
CPSSM
JN Dybowski dataset
dskernel

Department of Computational Biology, Indraprastha Institute of Information Technology,New Delhi,India