Please visit https://nicolagulmini.github.io/NERVE/.
NERVE can be used as a stand alone verison taking advantage of Docker and Docker-compose in linux systems.
- install Docker following these instructions and the post-installation procedure
- install docker-compose as explained here
- clone repository:
git clone git@github.com:/FranceCosta/NERVE.git
- navigate to the correct folder:
cd NERVE
- Run NERVE (the first time it will take a few minutes)
./NERVE.sh --help
Expected output:
usage: NERVE.py [-h] [-a] [-ev] -g [-ml] [-mm] [-m] [-mpsl] -p1 [-p2]
[-paefilter] [-pacfilter] [-pl] [-rz] [-rl] [-s] [-ss]
[-tdl] [-vl] [-vir] [-wd] [-nd] [-id] [-dfd] [-ep]
[-m1l] [-m2l] [-m1ovr] [-m2ovr] [-prt]
Run vaccine candidate prediction
optional arguments:
-h, --help show this help message and exit
-a, --annotation Activation (True) or deactivation (False) of annotation module.
Uses DeepFri to retrieve protein functional onthologies
(default: True)
-ev, --e_value Expect-value used in blastp for immunity modules (default:
1e-10)
-g, --gram Negative (n) or positive (p) gram stain of the pathogen of
interest (default: None)
-ml, --minlength Minimal length required for shared peptides to be extracted in
comparison analyses versus human and/or mouse (default: 9)
-mm, --mismatch Maximal number of not compatible substitutions allowed in shared
peptides alignment windows of 'minlength' size in immunity
modules (default: 1)
-m, --mouse Activation (True) or deactivation (False) of the mouse immunity
module. This module compares proteome1 with mouse proteome and a
further analysis of the eventual shared peptides is carried out
as in the autoimmunity module (default: True)
-mpsl, --mouse_peptides_sum_limit
Parameter calculated in mouse module and used by select module.
Protein with 'sum of shared peptides of the i-protein with mouse
proteins/number of aminoacids of the i-protein' <=
mouse_peptides_sum_limit and with absence of match mhc-I and
Mhc-II mouse ligands are selected (default: 0.15)
-p1, --proteome1 Path to proteome or Uniprot proteome ID (see:
https://www.uniprot.org/proteomes/?query=&sort=score) (default:
None)
-p2, --proteome2 Path to proteome or Uniprot proteome ID (see:
https://www.uniprot.org/proteomes/?query=&sort=score) (default:
None)
-paefilter, --p_ad_extracellular_filter
Parameter of select module. Extracellular proteins with a
probability of adhesin (pad) lower than
p_ad_extracellular_filter are discarded (0.-1) (default: 0.38)
-pacfilter, --p_ad_no_citoplasm_filter
Parameter of select module. Non-cytoplasmic Proteins with a
probability of adhesin (pad) lower than p_ad_no_citoplasm_filter
are discarded (0.-1) (default: 0.46)
-pl, --padlimit Set the probability of adhesin (pad) value cut-off for proteins
with 'Unknown' localization in the select module. Thus, these
proteins with a pad value < cut-off are discarded (0.-1)
(default: 0.85)
-rz, --razor Activation (True) or deactivation (False) of the loop-razor
module. This module allows the recovery of protein vaccine
candidates, with more than 2 transmembrane domains, that would
otherwise be discarded in the select module. The longest loop
with minimum len == 'razlen' aa will replace the original
protein sequence for following NERVE steps (default: True)
-rl, --razlen Set minimal length of loop considered in loop-razor module
(default: 50)
-s, --select Activation (True) or deactivation (False) of select module,
which filters PVC from proteome1 (default: True)
-ss, --substitution
Maximal number of compatible substitutions allowed in shared
peptides alignment windows of 'minlength' size in immunity
modules (default: 3)
-tdl, --transmemb_doms_limit
Parameter of select module. Proiteins with trasmembrane domains
>= transmemb_doms_limit are discarded (default: 3)
-vl, --virlimit Cut-off value for NERVirulent in the select module (0.-1)
(default: 0.5)
-vir, --virulent Activation (True) or deactivation (False) of NERVirulent module,
predictor of the probability of being a virulence factor
(default: True)
-wd, --working_dir
Path to working directory. If not existing, a working directory
with the given path is created (default: ./)
-nd, --NERVE_dir Path to NERVE repository folder (download from:
https://github.com/nicolagulmini/NERVE) (default:
/usr/nerve_python/NERVE)
-id, --iFeature_dir
Path to iFeature repository folder (download from:
https://github.com/Superzchen/iFeature) (default:
/usr/nerve_python/assets/iFeature)
-dfd, --DeepFri_dir
Path to DeepFri folder (download from:
https://github.com/flatironinstitute/DeepFRI) (default:
/usr/nerve_python/assets/DeepFri)
-ep (epitope prediction module), [True, False, default=True];
-m1l (mhc1 ligands length), [9,10,11, default=9];
-m2l (mhc2 ligands length), [9,11,13,15, default=11];
-m1ovr (mhc1 ligands max overlap), [1,2,default=1];
-m2ovr (mhc2 ligands max overlap), [1,2, default=1];
-prt (epitope binders percentile), [float, default=0.80]
Example run:
./NERVE.sh -p1 UP000002493 -g n -wd ./UP000002493