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Output format

DESCRIPTION

In the header of the out is indicated which prediction method and HLA allele were selected, as well as the corresponding two threshold values defining high binding peptides, and weak binding peptides. For Artificial neural network prediction high binding peptides have an IC50 value below 50 nM, and weak binding peptides an IC50 values below 500 nM. For weight matrix prediction high binding peptides have a prediction score greater than the 0.1% precentile score value of 1.000.000 random natural peptides, and weak binding peptides a score value above the 1% percentile score of 1.000.000 random natural peptides.

In the header is a link to an .xls file which contains the output in a tab seperated text file. For the format of this file see: Description of xls file.

For Artificial Neural network (ANN) prediction the output consists of 6 columns. For weight matrix predictions the output consists of 5 columns:

Residue number.

Peptide sequence (9mer)

Prediction score (called 1-log50K(aff) for ANN predictions)

Affinity as IC50 value in nM (only for ANN predictions)

Bind Level (WB for weak binder, SB for strong binder)

Sequence name

The predictions for each protein are summarized with a line stating the number of high and weak binding peptides identified.

EXAMPLE OUTPUT

Using this fasta input:

>Sequencename
SLYNTVATLISINTHISLANGHDAKAK

choosing peptide length 9, and the two alleles HLA-A*0201 and HLA-B*5801 will generate the following outputs:

HTML Output

Monday March 31 2008 10:41 NetMHC version 3.0. 9mer predictions using Artificial Neural Networks. Allele A0201. Strong binder threshold 50 nM. Weak binder threshold score 500 nM Download output sheet ---------------------------------------------------------------------------------------------------- pos peptide logscore affinity(nM) Bind Level Protein Name Allele ---------------------------------------------------------------------------------------------------- 0 SLYNTVATL 0.529 162 WB Sequencename A0201 1 LYNTVATLI 0.069 23754 Sequencename A0201 2 YNTVATLIS 0.025 38065 Sequencename A0201 3 NTVATLISI 0.328 1431 Sequencename A0201 4 TVATLISIN 0.022 39218 Sequencename A0201 5 VATLISINT 0.050 29197 Sequencename A0201 6 ATLISINTH 0.014 43052 Sequencename A0201 7 TLISINTHI 0.651 43 SB Sequencename A0201 8 LISINTHIS 0.062 25445 Sequencename A0201 9 ISINTHISL 0.161 8805 Sequencename A0201 10 SINTHISLA 0.344 1203 Sequencename A0201 11 INTHISLAN 0.006 46655 Sequencename A0201 12 NTHISLANG 0.014 43114 Sequencename A0201 13 THISLANGH 0.002 48981 Sequencename A0201 14 HISLANGHD 0.005 47346 Sequencename A0201 15 ISLANGHDA 0.039 32840 Sequencename A0201 16 SLANGHDAK 0.039 32797 Sequencename A0201 17 LANGHDAKA 0.082 20602 Sequencename A0201 18 ANGHDAKAK 0.001 49359 Sequencename A0201 -------------------------------------------------------------------------------------------------- NetMHC version 3.0. 9mer predictions using Artificial Neural Networks. Allele B5801. Strong binder threshold 50 nM. Weak binder threshold score 500 nM Download output sheet ---------------------------------------------------------------------------------------------------- pos peptide logscore affinity(nM) Bind Level Protein Name Allele ---------------------------------------------------------------------------------------------------- 0 SLYNTVATL 0.071 23245 Sequencename B5801 1 LYNTVATLI 0.052 28467 Sequencename B5801 2 YNTVATLIS 0.039 32889 Sequencename B5801 3 NTVATLISI 0.072 22920 Sequencename B5801 4 TVATLISIN 0.020 40058 Sequencename B5801 5 VATLISINT 0.037 33503 Sequencename B5801 6 ATLISINTH 0.046 30393 Sequencename B5801 7 TLISINTHI 0.145 10428 Sequencename B5801 8 LISINTHIS 0.028 36879 Sequencename B5801 9 ISINTHISL 0.488 255 WB Sequencename B5801 10 SINTHISLA 0.020 40293 Sequencename B5801 11 INTHISLAN 0.024 38758 Sequencename B5801 12 NTHISLANG 0.018 41116 Sequencename B5801 13 THISLANGH 0.021 40026 Sequencename B5801 14 HISLANGHD 0.020 40200 Sequencename B5801 15 ISLANGHDA 0.062 25526 Sequencename B5801 16 SLANGHDAK 0.017 41400 Sequencename B5801 17 LANGHDAKA 0.068 23994 Sequencename B5801 18 ANGHDAKAK 0.013 43595 Sequencename B5801 --------------------------------------------------------------------------------------------------

Description of xls file

This file always contains the predicted peptides in the order they appeared in the input file. The output data for each peptide will be displayed on a single line with predictions for each of the selected alleles in different columns.

The above FASTA input will give the following output when opened in Microsoft Excel:

Column 1: The name of the protein
Column 2: The position of the peptide within the full sequence
Column 3: The sequence of the subpeptide for which the prediction is made
Column 4 to
Column N: The predicted affinity of the peptide to the MHC expressed by each of the chosen alleles
Column N+1: An arbitrary mean score over all alleles. Useful for sorting peptides that binds to more than one allele.

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This file was last modified Wednesday 12th 2013f June 2013 11:23:17 GMT

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