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netMHCpan-4.1.readme
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netMHCpan-4.1.readme
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NetMHCpan 4.1 INSTALLATION INSTRUCTIONS
DESCRIPTION
The NetMHCpan 4.1 software predicts binding of peptides to any
known MHC molecule using artificial neural networks (ANNs). The
method is trained on a combination of more than 850,000 quantitative
Binding Affinity (BA) and Mass-Spectrometry Eluted Ligands (EL)
peptides. The BA data covers 201 MHC molecules from human (HLA-A, B,
C, E), mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo), swine
(SLA) and equine (Eqca). The EL data covers 289 MHC molecules from
human (HLA-A, B, C, E), mouse (H-2), cattle (BoLA), primates (Patr,
Mamu, Gogo), swine (SLA), equine (Eqca) and dog (DLA). Furthermore,
the user can obtain predictions to any custom MHC class I molecule
by uploading a full length MHC protein sequence. Predictions can be
made for peptides of any length.
Version 4.1 is described in the following publication:
NetMHCpan-4.1 and NetMHCIIpan-4.0: Improved predictions of MHC antigen
presentation by concurrent motif deconvolution and integration of MS
MHC eluted ligand data.
Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters and Morten Nielsen
Submitted, 2020
Earlier Version. 4.0:
NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions
Integrating Eluted Ligand and Peptide Binding Affinity Data
Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters,
and Morten Nielsen
The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893
The original paper:
NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any
HLA-A and -B Locus Protein of Known Sequence.
Morten Nielsen et al.
PLoS ONE 2(8): e796. doi:10.1371/journal.pone.0000796, 2007.
More information about the method, including instructions, guidelines, and
output description can be found at:
http://www.cbs.dtu.dk/services/NetMHCpan/
DOWNLOAD
The netMHCpan 4.1 software package is a property of Department of
Health Technology, Section of Bioinformatics The Technical University
of Denmark It may be downloaded only by special agreement.
For academic users there is a download site at:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan
Other users are requested to contact [email protected].
PRE-INSTALLATION
netMHCpan 4.1 currently runs under Darwin (MacOSX), and Linux.
The package consists of two files:
netMHCpan-4.1.readme this file
netMHCpan-4.1.<unix>.tar.gz compressed TAR archive
where 'unix' is the UNIX platform on which you are about to install. After
installation the software will occupy less than 45 MB of diskspace.
INSTALLATION
1. Uncompress and untar the package:
cat netMHCpan-4.1.<unix>.tar.gz | uncompress | tar xvf -
This will produce a directory 'netMHCpan-4.1'.
2. From the CBS website download the file:
https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz
Put it in the 'netMHCpan-4.1' directory and
then untar it:
tar -xvf data.tar.gz
This will produce a directory 'data'. It is necessary for the
NetMHCpan 4.1 software to operate; once it is installed you may delete
the 'data.tar.gz' file; it will not be needed.
2. In the 'netMHCpan-4.1' directory edit the script 'netMHCpan':
a. At the top of the file locate the part labelled "GENERAL SETTINGS:
CUSTOMIZE TO YOUR SITE" and set the 'NMHOME' variable to the full
path to the 'netMHCpan-4.1' directory on your system;
b. Set TMPDIR to the full path to the temporary directory of you choice. It must
be user-writable. You may for example set it to $NMHOME/tmp (and create
the tmp folder in the netMHCpan-4.1 directory).
3. In the 'netMHCpan-4.1/test' directory test the software:
> ../netMHCpan -p test.pep > test.pep.myout
> ../netMHCpan test.fsa > test.fsa.myout
> ../netMHCpan -hlaseq B0702.fsa -p test.pep > test.pep_userMHC.myout
> ../netMHCpan -p test.pep -BA > test.pep_BA.out
> ../netMHCpan -p test.pep -BA -xls -a HLA-A01:01,HLA-A02:01 -xlsfile my_NetMHCpan_out.xls
The resulting ".myout" files should not differ from the corresponding
".out" files provided in the package other than in the directory names
and small rounding errors.
4. Finish the installation:
a. Copy or link the 'netMHCpan' file to a directory in the users' path.
b. Copy the 'netMHCpan.1' file to a location in your manual system. If
you need a compiled version try running:
man -d netMHCpan.1 | compress >netMHCpan.Z
or:
neqn netMHCpan.1 | tbl | nroff -man | col | compress >netMHCpan.Z
5. Enjoy ...
PROBLEMS
Contact [email protected] in case of problems.
Questions on the scientific aspects of the netMHCpan method should be sent
to Dr. Morten Nielsen, [email protected].
DTU, 24 April 2020
M. Nielsen