HLAthena License

HLAthena is made available for use under the terms of this license.

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Inputs

Parameter name	Values	Description
alleles	click on one or more alleles from the drop-down list	The list of allele(s) for which predictions will be run
peptides	Type or paste peptides into the input box or load a file (sample input files provided)	A list or file containing the input peptides that predictions should be computed for. This can be either in a peptide format (i.e. one peptide per line) or in a fasta format. Please see below for more details.
Peptide column name	e.g. “pep”	The name of the column with peptide sequences
Context available?	“yes” or “no”	Specifies whether peptide context data exists in the input file. See also the more detailed description of the input file format below
Expression column name:	e.g. “TPM”	The name of the column containing peptide expression level; or blank if this information is not available. See also the more detailed description of the input file format below
Log-transform expr?	“yes” or “no”	Should the expr_col_name  be log transformed or not. See also the more detailed description of the input file format below
Aggregate by peptide?	“yes” or “no”	Should the input be aggregated in case the same peptide sequence appears multiple times. For example, the same peptide sequence could sometimes be derived from multiple source proteins and hence it can appear in the input file with different context sequences or with different expression values. Setting this parameter to “true” will aggregate the input on the peptide sequences and provide a single final scores for each peptide. String columns are semi-column concatenated, cleavability (and other numerical columns) is averaged, and expression is summed
Assign peptides to alleles by:	“ranks” or “scores”	The workflow will provide both log-likelihood presentation scores ([0,1], 1 is good) as well as percentile ranks ([0, 100], 0 is good). If multiple alleles are provided, the workflow will pick the best allele for each peptide. The best allele will be determined either based on “scores” or based on “ranks” depending on the value of this input
Threshold:	e.g. “0.1”	Set the threshold value for assigning a peptide to an allele. For example if assign_by_ranks_or_scores is set to “ranks” assign_threshold can be set to “0.1” which means that a peptide will be assigned to an allele if it scores within the top 0.1 percentile amongst a large set of background decoys. Alternatively, if assign_by_ranks_or_scores is set to “ranks” assign_threshold can be set to “0.98”.

 

peptide input file format details

A file containing the input peptides that predictions will be computed for. This can be either in a peptide format (i.e. one peptide per line) or in a fasta format:

1. peptide format

   The peptide format should be tab-delimited and it should contain a header line. The file can contain peptides of different lengths, lengths 8, 9, 10, and 11 are supported. If a peptide or context sequence contains non-standard amino acid symbols the corresponding row will be excluded from the analysis.

   Example:

   pep	ctex_up	ctex_dn	TPM
   AADIFYSRY	AAAAAAAAAGAGGGGFPHPAAAAAGGNFSV	AANQCRNLMAHPAPLAPGAASAYSSAPGEA	1.5
   AADLNLVLY	AAAAAAAAGAGGGGFPHPAAAAAGGNFSVA	ANQCRNLMAHPAPLAPGAASAYSSAPGEAP	8.3
   AADLVEALY	AAAAAAAGAGGGGFPHPAAAAAGGNFSVAA	NQCRNLMAHPAPLAPGAASAYSSA——	12.5
   AIDEDVLRY	—AAAALVSDSFSCGGSPGSSAFSLTSSS	AASSSPFANDYSVFQAPGVSGGSGGGGGGG	0.5
   IDLLKEIY	AAAAAALVSDSFSCGGSPGSSAFSLTSSSA	ASSSPFANDYSVFQAPGVSGGSGGGGGGGG	30.2

    

   The only required column is the peptide column, this is the column that contains peptide sequence (see peptide_col_name). If only this column is provided then only the MSintrinsic (or MSi) predictors will be ran. If exists_ctex is set to “true” and the file also contains ctex_up and ctex_dn columns then the MSiC predictor will also be ran. The ctex_up and ctex_dn columns should contain the 30 upstream and 30 downstream amino acid residues for each peptide. If the peptide is found at the boundary of a protein (i.e. N- or C-terminus) such that less than 30 residues are available in the source sequence, then ctex_up and ctex_dn should be padded with dashes '-'.

   Similarly, if exists_expr is set to true, the MSiCE models will be ran as well. Expression should be provided as TPM (transcripts per million) values or log(TPM+1) values. The column name containing the expression information is specified by the expr_col_name input. These values will be log-transformed if logtransform_expr is set to “true”.

   If the input file contains any other columns they will be carried through to the final predictions output file, with the exception of a few column names that are used internally that may be removed.

    

2. fasta format

   The fasta format input is assumed to follow standard fasta formatting. In addition we assume amino acid sequence are provided (rather than codon sequences). Spaces within the sequence are accepted, and so are both upper and lower case AA letters.

   Example:

   >HPV-16 E7
   mhgdtptlhe ymldlqpett dlycyeqlnd sseeedeidg pagqaepdra hynivtfcck cdstlrlcvq sthvdirtle dllmgtlgiv cpicsqkp
   >KRAS_G12D
   MTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLL

    

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Output columns

Column name	Description
model_<allele>	The type of model used for this {allele, length} combination, either allele-and-length specific or pan-allele-pan-length model
MSi_<allele>	The predicted score for this allele [0,1], 1 is good
prank.MSi_<allele>	The percentile ranks corresponding to the predicted score for this allele [0,100], 0 is good
MSiC_<allele>; MSiCE_<allele>	Analogous as above, for the MSiC and MSiCE models if expression and sequence context data is available and the exists_ctex and exists_expr input options were set to true
prank.MSiC_<allele>; prank.MSiCE_<allele>	Analogous to above for the , for the MSiC and MSiCE models
best.<model>	The best model score across input alleles. model here is one of MSi, MSiC, MSiCE, where the most integrative model available is considered. Note that the best score does not necessarily satisfy the allele assignment threshold
best.<model>_allele	The allele which corresponds to the best score
assign.<model>_ranks OR assign.<model>_scores	Depending on the value of *assign_by_ranks_or_scores* one of these two columns will be present in the output file. The numerical values of the score or rank which satisfy the threshold criteria set for peptide-to-allele assignment, or “NA” if none of the input alleles do
assign.<model>_allele	The allele(s) which satisfy the threshold criteria set for peptide-to-allele assignment, or “unknown” if none of the input alleles do

 

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Sample data files

Sample data files can be downloaded from the left-hand side menu in both peptide and fasta formats.

 

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Questions

If you have further questions regarding HLAthena please reach out on the gate.io logo.