Published June 29, 2023
| Version 1.0
Dataset
Open
Consensus nucleotide sequences for env and gag for paper: Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models
Creators
- 1. Max Planck Institute for Informatics
- 2. Fraunhofer Institute for Biomedical Engineering
- 3. 1. Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa 2. National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
- 4. Seq IT GmbH & Co.KG, Kaiserslautern, Germany
- 5. Institute of Immunology and Genetics, Kaiserslautern, Germany
- 6. Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Germany
Description
This is the consensus sequence repository to the manuscript "Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models".
It contains the 10% consensus nucleotide sequences of the env and gag (only p24) protein of HIV-1 used for the training and leftout data set. The NGS sequences are available under BioProject ID PRJNA810303 and the corresponding BioSample Accession IDs are SAMN26241863:26242168 and SAMN28728524:SAMN28728529
- env_leftout.fasta
- A fasta file that contains the consensus nucleotide sequences for the env protein for the leftout data set
- env_nt_274.fasta
- A fasta file that contains the consensus nucleotide sequences for the env protein for the training data set
- gag_leftout.fasta
- A fasta file that contains the consensus nucleotide sequences for the gag protein for the leftout data set
- gag_nt_274.fasta
- A fasta file that contains the consensus nucleotide sequences for the gag protein for the training data set
Files
Files
(1.0 MB)
| Name | Size | Download all |
|---|---|---|
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md5:136b8e3f89542f114cd932829af521c2
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98.4 kB | Download |
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md5:63e8db7ca8e65065ce87c4c11d28fb4f
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707.6 kB | Download |
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md5:32e1ae935b4e85285588872c58f12adf
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27.1 kB | Download |
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md5:00039e4e11c60b9f88a561da4deec990
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195.5 kB | Download |
Additional details
Related works
- Continues
- Dataset: 10.5281/zenodo.6797722 (DOI)
- Is supplement to
- Preprint: 10.1101/2022.07.06.498925 (DOI)