Skip to content
This repository has been archived by the owner. It is now read-only.
No description, website, or topics provided.
Branch: master
Clone or download
Pull request Compare This branch is 1 commit ahead of ComputationalBiophysicsCollaborative:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
README.md
in.exper.fullseq
in.exper.reduce4.seq
in.exper.weights
pr.exper.fullseq
pr.exper.reduce4.seq
pr.exper.weights
pr.naive.fullseq
pr.naive.reduce4.seq
pr.naive.weights
rt.exper.fullseq
rt.exper.reduce4.seq
rt.exper.weights

README.md

This code is associated with the paper from Biswas et al., "Epistasis and entrenchment of drug resistance in HIV-1 subtype B". eLife, 2019. http://dx.doi.org/10.7554/eLife.50524

elife data

The files contained in here are the processed data files used to infer the Potts models and annotated as below:

Protease (PR)

  • pr.exper.fullseq : Alignment of our processed drug-experienced HIV-1 subtype B Protease sequences (obtained from the Stanford HIVDB) in the full 20-letter amino acid.

  • pr.exper.reduce4.seq : Alignment of our processed drug-experienced HIV-1 subtype B Protease sequences in the reduced 4-letter (ABCD) amino acid alphabet as used to infer the drug-experienced Potts model.

  • pr.exper.weights : Sequence weights of individual sequences in pr.exper.fullseq or pr.exper.reduce4.seq. Sequences are given weights such that the effective number of sequences obtained from a single patient is 1.

  • pr.naive.fullseq : Alignment of our processed drug-naive HIV-1 subtype B Protease sequences (obtained from the Stanford HIVDB) in the full 20-letter amino acid.

  • pr.naive.reduce4.seq : Alignment of our processed drug-naive HIV-1 subtype B Protease sequences in the reduced 4-letter (ABCD) amino acid alphabet as used to infer the drug-naive Potts model.

  • pr.naive.exper.weights : Sequence weights of individual sequences in pr.naive.fullseq or pr.naive.reduce4.seq. Sequences are given weights such that the effective number of sequences obtained from a single patient is 1.

Reverse Transcriptase (RT)

  • rt.exper.fullseq : Alignment of our processed drug-experienced HIV-1 subtype B RT sequences (obtained from the Stanford HIVDB) in the full 20-letter amino acid.

  • rt.exper.reduce4.seq : Alignment of our processed drug-experienced HIV-1 subtype B RT sequences in the reduced 4-letter (ABCD) amino acid alphabet as used to infer the Potts model.

  • rt.exper.weights : Sequence weights of individual sequences in rt.exper.fullseq or rt.exper.reduce4.seq. Sequences are given weights such that the effective number of sequences obtained from a single patient is 1.

Integrase (IN)

  • in.exper.fullseq : Alignment of our processed drug-experienced HIV-1 subtype B IN sequences (obtained from the Stanford HIVDB) in the full 20-letter amino acid.

  • in.exper.reduce4.seq : Alignment of our processed drug-experienced HIV-1 subtype B IN sequences in the reduced 4-letter (ABCD) amino acid alphabet as used to infer the Potts model.

  • in.exper.weights : Sequence weights of individual sequences in in.exper.fullseq or in.exper.reduce4.seq. Sequences are given weights such that the effective number of sequences obtained from a single patient is 1.

You can’t perform that action at this time.