transmembrane domains in proteins); Phobius 1.01 [13] (predicts
transmembrane topology and signal peptides); DeepLoc 1.0 [14]
(predicts eukaryotic protein subcellular localization using deep
learning); and IEDB peptide–MHC binding predictors (MHCI
version 2.17 and MHCII version 2.16.3) [15] (see Note 1).
Observe that each of the seven programs have specific version
numbers on which Vacceed has been tested. There is no assurance
older or newer program versions will work.
The most pertinent file from a user’s perspective is a species
configuration file in a header-key format (see Fig. 1). For example,
[Resources] is the header, and “name” is the key. Text following the
“¼” sign is configurable. A suggested convention is to have one
configuration file for each target pathogen. Vacceed is started by
entering only one command in a Linux Shell (or terminal) (e.g.,
perl startup xx, where xx is a user specified code that links Vacceed to
the target pathogen configuration file). No other commands are
required.
Fig. 1 Extract from a species configuration file
Eukaryotic Pathogen Antigen Discovery Using Vacceed
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