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Table 2 In silico analysis - bioinformatic tools and databases

From: In silicoanalysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers

Tool URL Description
NetMHCpan http://www.cbs.dtu.dk/services/NetMHCpan/ A server for predicting the binding of peptide sequences to MHC molecules (class I) for humans and other species
NetMHCIIpan http://www.cbs.dtu.dk/services/NetMHCIIpan/ A server for predicting the binding of peptide sequences to MHC molecules (class II) for humans and other species
Immune Epitope Database (IEDB) http://www.immuneepitope.org/ A database storing data related to antibody and T-cell epitopes for humans, non-human primates, rodents, and other animal species
Allele Frequency Net Database (AFND) http://www.allelefrequencies.net/ A database storing allele, haplotype and genotype frequencies in worldwide populations, sourced from over 1,200 studies, concerning immune-related genes (HLA, KIR, MIC and cytokine gene polymorphisms)
PyPop http://www.pypop.org/ Open-source software package for the analysis of populations at large scale and multiple loci
GraphViz http://www.graphviz.org/ Open source graph visualization software
dbMHC http://www.ncbi.nlm.nih.gov/gv/mhc/main.cgi?cmd=init A database providing DNA, protein and clinical data related to the human major histocompatibility complex (MHC)
PHYLIP http://evolution.genetics.washington.edu/phylip.html Open source software for inferring phylogenies
TreeView http://taxonomy.zoology.gla.ac.uk/rod/treeview.html Open source tree viewing software
  1. KIR, Killer-cell immunoglobulin-like receptors; MIC, MHC class I chain related (MIC) genes.