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
- -merLength k
- -withinDOfCenter d
- -hlaSet [singleton OR supertype OR all]
- -showBy [all OR hla OR length OR hlaAndLength OR doNotGroup]
- -model LANLIEDB03062007
The web version of this tool uses a different predictive model.
This desktop version offers more options for scanning.
Each line of the input should be of the form
peptide <TAB> hla ... [when "-hlaSet singleton" is given]
peptide <TAB> supertype ...[when "-hlaSet supertype" is given]
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
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
- If "-inputHasHeader" is given, the first line of the input is threated as a header.
- "-merLength k", where k is "scan" (default), "8", "9", "10", "11", or "given"
- With "scan" all lengths are scanned.
- With a numeric value, only mers of that length are scanned
- With "given" there is no scanning; the whole input peptide is scored.
- In all cases, an adjustment is made to correct for the relative frequency of the length/hla pair.
- "-withinDOfCenter d" where d is an integer or null (default)
- When an integer this limits the scan for epitopes to mers such that
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.
- "-hlaSet singleton" (default) means to use the hla from the file
- "-hlaSet supertype" means use the supertype from the file, scanning all its hlas
- "-hlaSet all" means to scan all known hlas
Among the hlas considered, the best will be reported
- "-modelOnly" if given then uses the model's probability even if a peptide is on a source list.
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
- "-showBy" tells how to report the maximum probability prediction(s)
- "-showBy all" (default) - for each input line, reports the maximum probability prediction(s).
- "-showBy hla" - for each input line and hla, reports.
- "-showBy length" - for each input line and peptide length, reports.
- "-showBy hlaAndLength" - for each input line and hla and peptide length, reports.
- "-showBy doNotGroup" - for each input line, reports every prediction.
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:
- HLA (if hla is not given)
- BestNFlank (for the LANLIEDB03062007 model, always empty because it doesn't use flanking regions)
- BestCFlank (for the LANLIEDB03062007 model, always empty because it doesn't use flanking regions)
- FlankingLength (for the LANLIEDB03062007 model, always 0)
- Source (for the LANLIEDB03062007 model, LANL and/or IEDB)
, and J. Listgarten
, "Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope
," RECOMB 2006