The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species.

This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB. The webservices are described at: http://tools.immuneepitope.org/main/tools-api/ That page also describes how to retrieve the available HLA alleles for class of epitope binding.

INPUTS

peptide sequences from a fasta file or a column in a tabular file

HLA alleles either entered as text or one per line in a text file

OUTPUTS

A tabular file containing the results returned from the IEDB web service

Typical Workflow for Human MHC I Binding Prediction

The RNAseq data for the subject would be used for:

• HLA prediction by seq2HLA
• Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta

The seq2HLA ClassI.HLAgenotype4digits output:

Needs to be converted into IEDB formatted alleles:

In the workflow above QueryTabular tool converts the alleles:

• Filter Dataset Input
  • skip leading lines - skip lines: 1
  • select columns - columns: 2,4
  • regex replace value in column - column: 1 regex pattern: ^(\w+[*]\d\d:\d\d\d?).*$ replacement expression: HLA-\1
  • regex replace value in column - column: 2 regex pattern: ^(\w+[*]\d\d:\d\d\d?).*$ replacement expression: HLA-\1
• SQL Query to generate tabular output
  • SELECT c1 FROM t1 UNION SELECT c2 FROM t1

The IEDB formatting can also be performed by TextProcessing tools:

The TextProcessing steps to convert the alleles:

• Remove beginning - removes the header line
• Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line
  • Find pattern: ^.*\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\t.*\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\t.*$
  • Replace with: HLA-\1\nHLA-\2
• Unique - remove duplicates