The Protmapper maps references to protein sites to the human reference sequence based on UniProt, PhosphoSitePlus, and manual curation.
The Protmapper is a Python package that is available on PyPI and can be installed as:
pip install protmapper
Alternatively, the Protmapper Docker container can be run to expose it as a REST API as:
docker run -d -p 8008:8008 labsyspharm/protmapper:latest
In addition to supporting usage via a Python API and a REST service, Protmapper also provides a command line interface that can be used as follows.
Run Protmapper on a list of proteins with residues and sites provided in a
text file.
positional arguments:
input Path to an input file. The input file is a text file
in which each row consists of four comma separated
values, with the first element being a protein ID, the
second, the namespace in which that ID is valid
(uniprot or hgnc),third, an amino acid represented as
a single capital letter, and fourth, a site position
on the protein.
output Path to the output file to be generated. Each line of
the output file corresponds to a line in the input
file. Each linerepresents a mapped site produced by
Protmapper.
optional arguments:
-h, --help show this help message and exit
--peptide If given, the third element of each row of the input
file is a peptide (amino acid sequence) rather than a
single amino acid residue. In this case, peptide-
oriented mappings are applied. In this mode the
following boolean arguments are ignored.
--no_methionine_offset
If given, will not check for off-by-one errors in site
position (possibly) attributable to site numbering
from mature proteins after cleavage of the initial
methionine.
--no_orthology_mapping
If given, will not check sequence positions for known
modification sites in mouse or rat sequences (based on
PhosphoSitePlus data).
--no_isoform_mapping If given, will not check sequence positions for known
modifications in other human isoforms of the protein
(based on PhosphoSitePlus data).
For a detailed documentation of the Protmapper, visit http://protmapper.readthedocs.io
The development of protmapper is funded under the DARPA Automated Scientific Discovery Framework project (ARO grant W911NF018-1-0124).