Epipred.exe

Usage

Epipred optionalParameters inputFile outputFile
Epipred -help

For each line of input, reports the most likely epitope(s). In case of ties, combines result into one line.

where the optional parameters are

Web Version

The web version of this tool uses a different predictive model.

http://atom.research.microsoft.com/bio/epipred.aspx

This desktop version offers more options for scanning.

Input


Each line of the input should be of the form

peptide <TAB> hla ... [when "-hlaSet singleton" is given]
OR
peptide <TAB> supertype ...[when "-hlaSet supertype" is given]
OR
peptide ... [when "-hlaSet all" is given]

Additional fields will be echoed to output. If a header is given, it
must have columns for at least peptide and, if given, hla or supertype

Sample Input

For the LANLIEDB03062007 model, HLA's must be of the form of A,B, or C followed by two digits, except for HLAs that start A68 or B15 which must be of four digits.

Supertype table used by the LANLIEDB03062007 model

Optional Parameters

at least one edge of the mer is within d amino acids of the center
of the peptide given for scanning. If the input peptide has even
length, we use left of center for center.
Among the hlas considered, the best will be reported
Otherwise, peptides on a source list are given a probability of 1.0.
(The "source list" is the list of epitopes and HLAs used to train the model.
The source list for model LANLIEDB03062007

Output

The output is a header line followed by one output line for each input line.
Additional fields are inserted after the required inputs, the fields are:

Sample Output

Reference

Reference:
D. Heckerman, C. Kadie, and J. Listgarten, "Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction," RECOMB 2006.