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. 2008 Sep;24(9):1215–1220. doi: 10.1089/aid.2008.0009

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Copyright 2008, Mary Ann Liebert, Inc.

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FIG. 2. — Prediction of coreceptor usage by R5X4 V3 sequences using bioinformatic prediction algorithms. (A) Unique R5X4 V3 amino acid sequences (n = 30) from 17 patients were aligned using ClustalX. The sequences are shown aligned to the CCR5-tropic Clade B consensus sequence. Sequences are grouped by patient. Sequences derived from brain (n = 4) are underlined. Positions 11 and 25 in the V3 loop are highlighted in the sequence alignments. Algorithms that correctly predict the ability to use CXCR4 are indicated following each sequence. 1 = 11/24/25 rule; 2 = charge rule; 3 = PSSM (X4R5); 4 = PSSM (SINSI); 5 = random forest; 6 = SVM_genomiac; 7 = SVM_geno2pheno. (B) Summary of total number of correct predictions for each bioinformatic algorithm and the program's specificity for the 30 R5X4 V3 sequences.