Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

HIValg Program: Sequence Analysis

There are two methods for indicating which algorithms you would like to have run on your input sequences. You can use any of them in combination. Choose one or more of the default algorithms and/or upload a user-created algorithm in ASI2 format.

Algorithms
 

Selection Input

Select one or more previously published algorithms using the checkboxes below.
ANRSV2013.09     HIVDB     RegaV9.1.0    

File Upload

Choose an ASI2-encoded interpretation algorithm from your computer using the file selection box below.


The ASI grammar definition has been updated and it is not backwards compatible; so please follow the documentation on converting your rules from the old format to the new ASI2 grammar.

Sequence information can be entered in FASTA, plain text, or GRF (Bayer Diagnostics) format. Sequences in FASTA format or plain text can be pasted in the text box (option A) or uploaded (option B). GRF files can only be uploaded (option C). Using options A or B, it is possible to analyze up to 100 sequences at a time (character limit:600,000). Example data set: a small set (n=10)

The output can be customized to display the results using the original interpretation of each algorithm or a normalized interpretation in which the 3 levels of the ANRS and Rega are assigned Susceptible (S), Intermediate (I), Resistant (R) and the HIVDB levels are mapped to SIR: Susceptible, Potential Low-Level => S; Low-level, Intermediate => I; Resistant => R and an optional identifier and date. For further explanations and sample datasets please see the Release Notes.

Sequences
 

Text Input

Paste sequence text in the text box below.

Text File Upload

Choose a file to upload from your computer using the file selection box below.

GRF File Upload

Choose a GRF (Bayer Diagnostics) file to upload from your computer using the file selection box below.
Output Analysis:
Original        SIR        SpreadSheet
RESET
ANALYZE