Hypermut 2.0
Analysis & Detection of APOBEC-induced Hypermutation
Purpose: This interface takes a nucleotide alignment and documents the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence.
Details: The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. Please choose the reference sequence carefully. For example, for an intrapatient set, the reference should probably be the most common form in the first sampled time point; for a set of unrelated sequences, the reference should probably be the consensus sequence for the appropriate subtype. Before using, please read:
References: Please reference these articles when using Hypermut:
- Rose, PP and Korber, BT. 2000. Detecting hypermutations in viral sequences with an emphasis on G -> A hypermutation. Bioinformatics 16(4): 400-401.
- Bruno, WJ, Abfalterer, WP, Foley, BT, Leitner, TK and Korber, BT. Detection of hypermutation in HIV sequences using two context positions and avoiding nucleotide content effects. Manuscript submitted.
| These options apply only to Hypermut 2.0 analysis, and have no effect on the Original Hypermut output. For typical analyses of APOBEC-induced hypermutation in HIV, these options should be left in their default settings. | |||||
| Mutation | |||||
|---|---|---|---|---|---|
| Upstream context: | ↓ |
Downstream context: | Enforce context: | ||
| Customize Hypermut pattern: | ↓ |
On reference sequence On both sequences On query sequence | |||
| Customize control pattern: | ↓ | ||||
| Analyses to perform: | Both Original Hypermut Hypermut 2.0 |