Mutant peptide extractor and informer (MuPeXI)
Extracts user defined peptides lengths around missense variant mutations, indels and frameshifts from a VCF file. Information from each mutation is annotated together with the mutant and normal peptides in the file output.
For publication of results, please cite:
MuPeXI relies on binding predictions from NetMHCpan; for publication of results please cite NetMHCpan in addition to MuPeXI.
MuPeXI is available on GitHub.
Expression file:
Upload a tab-delimited file with expression values for each Ensembl transcript ID.
Format: Ensembl Transcript ID <tab> Expression value (TPM) <tab> variance on call.
This file can be obtained through RNAseq analysis with, for example, Kallisto.
Transcript IDs must correspond to the GRCh38 v78 coordinates.
At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
The prediction output for each peptide pair consists of the following columns:
M: Missense variant
I: Inframe insertion
D: Inframe deletion
F: Frameshift variant
NetMHCpan output
%Rank of prediction score to a set of 200.000 random natural 9mer peptides. For more information see the NetMHCpan4.0 output format.
# VERSION: MuPeXI 1.1 # CALL: /usr/cbs/bio/src/MuPeXI-1.1/mupexi/MuPeXI.py -c /usr/cbs/bio/src/MuPeXI-1.1/config.ini -w -m -v /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.0 -e /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.1 -a HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03 -l 9 # DATE: Monday 15 of August 2016 # TIME: 15:34:35 # PWD: /net/athena/usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7 HLA_allele Norm_peptide Norm_MHCAffinity Norm_MHCrank Mut_peptide Mut_MHCAffinity Mut_MHCrank Gene_ID Transcript_ID Amino_Acid_Change Allele_Frequency Mismatches peptide_position Chr Genomic_Position Protein_position Mutation_Consequence Gene_Symbol Cancer_Driver_Gene Expression_Level Mutant_affinity_score Normal_affinity_score Expression_score priority_Score HLA-B07:02 .L....... 13351.1 9.5 SPDLGGSKF 267.2 0.7 ENSG00000156510 ENST00000354624 L/P 0.784 1 2 10 69232785 83 M HKDC1 No 61.0165798 0.998498817743263 5.175555005801869e-17 1.0 78 HLA-A02:01 .R.R...D. 26906.1 32.0 KMYLKIVEV 8.7 0.1 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9999251537724895 7.175095973164411e-66 0.9841444919059494 64 HLA-C03:03 G......G. 5847.9 6.0 FSVIVCHKM 272.0 0.8 ENSG00000048028 ENST00000003302 FQ/X 0.650 2 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9975273768433653 2.0611536181902037e-09 0.9841444919059494 64 HLA-C07:02 A.I..E... 5100.7 4.0 MYLKIVEVI 1136.8 0.8 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9975273768433653 4.5397868702434395e-05 0.9841444919059494 64 HLA-A31:01 T...N.... 3096.9 6.0 KIVEVIQKR 99.7 0.9 ENSG00000048028 ENST00000003302 FQ/X 0.650 2 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.995929862284104 2.0611536181902037e-09 0.9841444919059494 64 HLA-C03:03 .....G.VY 4781.8 5.0 VIVCHKMYL 643.9 1.4 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9525741268224334 3.059022269256247e-07 0.9841444919059494 61 HLA-A31:01 ......DP. 1025.1 3.5 LFSVIVCHK 214.0 1.4 ENSG00000048028 ENST00000003302 FQ/X 0.650 2 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9525741268224334 0.0005527786369235996 0.9841444919059494 61 HLA-C07:02 QN...M... 9837.7 7.5 CKSFSICLL 2315.8 1.6 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.8807970779778823 1.1399918530430558e-12 0.9841444919059494 56 HLA-A31:01 T.F..R... 14.2 0.09 IVCHKMYLK 131.1 1.0 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.9933071490757153 0.9999288038061921 0.9841444919059494 56 HLA-A31:01 ....E.... 506.9 2.5 TILDKLVQR 68.3 0.6 ENSG00000156096 ENST00000305107 E/K 0.563 1 5 4 69495729 45 M UGT2B4 No 2.44878178 0.9990889488055994 0.07585818002124355 0.9878510119201874 53 HLA-A02:01 E........ 9137.4 13.0 KLVQRGHEV 162.5 1.4 ENSG00000156096 ENST00000305107 E/K 0.563 1 1 4 69495729 45 M UGT2B4 No 2.44878178 0.9525741268224334 1.299581425007503e-24 0.9878510119201874 53 HLA-C07:02 .....G.VY 8919.0 6.5 VIVCHKMYL 2701.8 1.9 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.6224593312018547 1.6918979223288784e-10 0.9841444919059494 40 HLA-C07:02 S..Y...L. 3438.9 2.5 NFEDLFSVI 2684.2 1.9 ENSG00000048028 ENST00000003302 FQ/X 0.650 3 1:9 11 113834326-113834329 181 F USP28 No 2.31471308 0.6224593312018547 0.07585818002124355 0.9841444919059494 39 HLA-B07:02 ...R..... 31.9 0.12 KPGCKTNQL 43.2 0.17 ENSG00000169925 ENST00000371834 R/C 0.333 1 4 9 134053378 34 M BRD3 Yes 1.86032922 0.9998937914787018 0.9999172827771484 0.9611149444887752 32 HLA-C07:02 R........ 1301.2 0.9 CKTNQLQYM 2021.9 1.4 ENSG00000169925 ENST00000371834 R/C 0.333 1 1 9
# VERSION: MuPeXI 1.1 # CALL: /usr/cbs/bio/src/MuPeXI-1.1/mupexi/MuPeXI.py -c /usr/cbs/bio/src/MuPeXI-1.1/config.ini -w -m -v /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.0 -e /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.1 -a HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03 -l 9 # DATE: Monday 15 of August 2016 # TIME: 15:34:35 # PWD: /net/athena/usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7 ---------------------------------------------------------------------------------------------------------- MuPeX ---------------------------------------------------------------------------------------------------------- Reading protein reference file: Found 99436 sequences, with 0 [9]mers of which 0 were unique peptides Reading VEP file: Found 22 irrelevant mutation consequences which were discarded Found 29 missense variant mutation(s) 0 insertion(s) 0 deletion(s) 3 frameshift variant mutation(s) In 7 genes and 32 transcripts Checking peptides: 0 peptides matched a normal peptide and were discarded 0 peptides included unsupported symbols (e.g. *, X, U) and were discarded Final Result: 390 potential mutant peptides MuPeX Runtime: 0:00:15.476422 ---------------------------------------------------------------------------------------------------------- MuPeI ---------------------------------------------------------------------------------------------------------- Reading through MuPex file: Found 390 peptides of which 105 were unique Detecting HLA alleles: Detected the following 6 HLA alleles: HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03 of which 6 were unique Running NetMHCpan 2.8: Analyzed 6 HLA allele(s) NetMHCpan runtime: 0:00:05.053376 MuPeI Runtime: 0:00:09.374437 TOTAL Runtime: 0:00:31.901699
>DTU|ENST00000436792_184838714|M_D9Y SAQIVSAAYKVDAGLPT >DTU|ENST00000422105_184838714|M_D9Y SAQIVSAAYKVDAGLPT >DTU|ENST00000452666_184838714|M_D9Y SAQIVSAAYKVDAGLPT >DTU|ENST00000380779_10567210|M_S9F AFDANTMTFAEKVLCQF >DTU|ENST00000424463_184838714|M_D9Y SAQIVSAAYKVDAGLPT >DTU|ENST00000510114_69495729|M_E9K MNIKTILDKLVQRGHEV >DTU|ENST00000610939_10567210|M_S9F AFDANTMTFAEKVLCQF >DTU|ENST00000446204_184838714|M_D9Y SAQIVSAAYKVDAGLPT >DTU|ENST00000512583_69495729|M_E9K MNIKTILDKLVQRGHEV >DTU|ENST00000305107_69495729|M_E9K MNIKTILDKLVQRGHEV >DTU|ENST00000317552_10567210|M_S9F AFDANTMTFAEKVLCQF >DTU|ENST00000545540_113834326-113834329|F_FQ9:51X FSAVIQSLNNCLNFEDLFSVIVCHKMYLKIVEVIQKREISCLCKSFSICLL >DTU|ENST00000426319_184838714|M_D9Y TFSEFNPYYKVDAGLPT
MuPeXI: Prediction of neo-epitopes from tumor sequencing data
Anne-Mette Bjerregaard, Morten Nielsen, Sine R. Hadrup, Zoltan Szallasi, Aron Charles Eklund
Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the Mutant Peptide Extractor and Informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI.
If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0). If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).
If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.
Correspondence:
Technical Support: