Genotype-Phenotype Datasets
Version 4.1, July 15, 2008
- To access high quality filtered datasets from HIVDB and analyses using methods described in the paper by Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW., Genotypic predictors of human immunodeficiency virus type 1 drug resistance.,Proceedings of National Academy of Sciences of the United States of America, Oct 25, 2006, click here.
- To access complete unfiltered datasets from HIVDB by gene and phenotype assay, click the links below:
| Description of fields in the datasets |
| Field Name | Description |
|---|
| SeqID | Sequence identifier |
| Subtype | Subtype of sequence |
| Method | Phenotype method |
| RefID | Published reference. View References Table |
| Type | Clinical vs. Lab Isolate. Lab isolates are site directed mutants or results of in vitro passage. |
| IsolateName | Isolate identifier |
| Drug Fold | Fold resistance of Drug X compared to the wild type. |
| Drug FoldMatch | Fold match for Drug X. '=' for most results. '<' if result is below the lower limit of the assay. '>' if the result is greater than the upper limit of the assay. |
| P1...P n | Amino acid at this position. '-' indicates consensus; '.' indicates no sequence; '#' indicates an insertion; '~' indicates a deletion; '*' indicates a stop codon and a letter indicates one letter Amino Acid substitution. Two and more amino acid codes indicates a mixture. The consensus B amino acid sequences can be found in http://hivdb.stanford.edu/pages/asi/releaseNotes/ |
| Mutation Lists | Mutation Lists provided at the far right of the output are lists of mutations present in the sequence. Some lists contain all the mutations, others contain specific sublists. |
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