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.
Protease, RT, and integrase mutations can be entered using either the text box or pull down menus (detailed usage is found below).
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.
To use the text box, type each mutation in uppercase separated by one or more spaces (the consensus wildtype amino acids and separating commas are optional). If there is a mixture of more than one amino acid at a position, write both amino acids (an intervening slash is optional). Use lowercase "ins" to indicate an insertion and lowercase "del" to indicate a deletion; if you type a mixture of "i/n/s" or "ins", this will be assumed to be an insertation rather than a mixture, to avoid this, enter this mixture in uppercase (likewise for "del"). Otherwise, lowercase mutations are allowed.
The pulldown menus are implemented with Javascript. Each pulldown menu lists amino acids known to be associated with drug resistance as well as amino acids at drug-resistance positions that occur with a frequency of >=0.1% among treated or untreated patients. To enter an amino acid not in the list, click on the asterisk "*". If you have trouble using Javascript on your browser or if you wish to enter a mixture, you should use the textbox instead.
