3  HLA Analysis Programs

Haplotype Analysis

BIGDAWG

Pappas et al. (2016)

https://github.com/IgDAWG/BIGDAWG

Hapl-o-Mat

Schäfer, Schmidt, and Sauter (2017)

https://github.com/DKMS/Hapl-o-Mat

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1692-y

Locus Analysis

midasHLA - Locus analysis

Migdal et al. (2021)

https://github.com/Genentech/midasHLA

Fine-Mapping

(Clay et al. 2022)

Peptide Binding

MHCcluster2.0

(Thomsen et al. 2013)

https://services.healthtech.dtu.dk/services/MHCcluster-2.0/

Docking Analysis

CB-Dock2

(Liu and Cao 2024)

(Liu et al. 2022)

https://cadd.labshare.cn/cb-dock2/

Clay, Selene M., Nathan Schoettler, Andrew M. Goldstein, Peter Carbonetto, Matthew Dapas, Matthew C. Altman, Mario G. Rosasco, et al. 2022. “Fine-Mapping Studies Distinguish Genetic Risks for Childhood- and Adult-Onset Asthma in the HLA Region.” Genome Medicine 14 (1): 55. https://doi.org/10.1186/s13073-022-01058-2.

Liu, Yang, and Yang Cao. 2024. “Protein-Ligand Blind Docking Using CB-Dock2.” Methods in Molecular Biology (Clifton, N.J.) 2714: 113–25. https://doi.org/10.1007/978-1-0716-3441-7_6.

Liu, Yang, Xiaocong Yang, Jianhong Gan, Shuang Chen, Zhi-Xiong Xiao, and Yang Cao. 2022. “CB-Dock2: Improved Proteinligand Blind Docking by Integrating Cavity Detection, Docking and Homologous Template Fitting.” Nucleic Acids Research 50 (W1): W159–64. https://doi.org/10.1093/nar/gkac394.

Migdal, Maciej, Dan Fu Ruan, William F. Forrest, Amir Horowitz, and Christian Hammer. 2021. “MiDASMeaningful Immunogenetic Data at Scale.” Edited by Mihaela Pertea. PLOS Computational Biology 17 (7): e1009131. https://doi.org/10.1371/journal.pcbi.1009131.

Pappas, Derek J., Wesley Marin, Jill A. Hollenbach, and Steven J. Mack. 2016. “Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An Integrated Case-Control Analysis Pipeline.” Human Immunology 77 (3): 283–87. https://doi.org/10.1016/j.humimm.2015.12.006.

Schäfer, Christian, Alexander H. Schmidt, and Jürgen Sauter. 2017. “Hapl-o-Mat: Open-Source Software for HLA Haplotype Frequency Estimation from Ambiguous and Heterogeneous Data.” BMC Bioinformatics 18 (1): 284. https://doi.org/10.1186/s12859-017-1692-y.

Thomsen, Martin, Claus Lundegaard, Søren Buus, Ole Lund, and Morten Nielsen. 2013. “MHCcluster, a Method for Functional Clustering of MHC Molecules.” Immunogenetics 65 (9): 655–65. https://doi.org/10.1007/s00251-013-0714-9.