NERVE

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nerve

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NERVE (New Enhanced Reverse Vaccinology Environment) is an open-source, reverse vaccinology environment, with which you can analyze bacterial proteomes in FASTA format to get the best protein vaccine candidates (PVCs) and their epitopes.

<p> The project was initially developed in Perl, in 2006, for Linux-users only. You can find more info about it in the related article, clicking on this link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1570458 </p> <p>

Now, we are carrying on this project independently from the original developer and this is the Github page of the NERVE 2.0-stand-alone version.

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Users can also leverage a user-friendly web-based graphical interface (GUI) hosted on our dedicated server: https://nerve-bio.org. This GUI empowers even novice users to operate NERVE with ease, requiring only the proteome FASTA file as input.

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It further enhances the experience by allowing visualization of analysis results using our custom-built visualizer, also facilitating the identification of epitopes (and their constituent parts) predicted to bind to multiple HLA alleles.

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Key features:

Machine Learning and Alignment Analysis, using ML methods for antigen analysis
Flexible Usage, customizing your settings
Stand-alone Docker Version, reducing dependencies for its installation
Intuitive Web-based GUI,
Complete Python Rewrite, enhancing its performance and maintainability.
Ongoing Development, continuously evolving with new features and improvements.
Comprehensive Output, including:
- a CSV file summarizing all candidate proteins with scores and predicted characteristics (P_adhesin, P_antigen, location, etc.).
- a separate CSV file listing discarded proteins.
- dedicated folders containing additional files (CSVs and PNGs) for each selected protein with predicted linear epitopes.

Benefits for Vaccine Research:

Accessibility: researchers worldwide can access and use NERVE without barriers, accelerating vaccine development efforts globally.
Transparency: allowing researchers to scrutinize the code, identify potential issues, and contribute to its refinement.
Collaboration: by enabling researchers to share, modify, and extend the pipeline, leading to innovative advancements.
Community-Driven Development: the open-source model encourages community participation, ensuring that NERVE remains aligned with the evolving needs of the vaccine research community.

Whether it's reporting bugs, suggesting improvements, or developing new features, your input is valuable.

We welcome contributions from researchers interested in shaping the future of NERVE!

Installation procedure of stand-alone version:

NERVE can be used as a stand alone version taking advantage of Docker in Linux systems.

1) Install Docker following these instructions.

2) Follow this post-installation procedure even if you already installed Docker.

2) Clone the repository:

git clone https://github.com/nerve-bio/NERVE.git

3) Navigate to the correct folder:

cd NERVE

4) Run NERVE (the first time it will take a few minutes)

./NERVE.sh --help

This is the expected output:

usage: NERVE.py [-h] [-a] [-ev] -g [-ml] [-mm] [-m] [-mpsl] -p1 [-p2] [-pl] [-rz] [-rl] [-s] [-ss] [-tdl] [-vl] [-vir]
                [-ep] [-m1l] [-m2l] [-m1ovr] [-m2ovr] [-prt] [-wd] [-nd] [-id] [-dfd] [-epp]

NERVE 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: False)
  -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)
  -pl, --padlimit   Set the probability of adhesin (pad) value cut-off for all proteins in select module. Thus, these proteins with a pad value < cut-
                        off are discarded (0.-1) (default: 0.5)
  -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: False)
  -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. Proteins 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: False)
  -ep, --epitopes   Activate or deactivate epitope prediction module (default: True)
  -m1l, --mhci_length 
                        mhci binders length (9, 10, 11 are available) (default: 9)
  -m2l, --mhcii_length 
                        mhcii binders length (9, 11, 12, 15 are available) (default: 11)
  -m1ovr, --mhci_overlap 
                        mhci-epitope overlap (default: 1)
  -m2ovr, --mhcii_overlap 
                        mhcii-epitope overlap (default: 1)
  -prt, --epitope_percentile 
                        percentile decision threshold on which to predict epitopes from full length proteins (default: 0.9)
  -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)
  -epp, --ep_plots  Epitopes plotting script (default: True)

5) (optional) test correct functioning:

pytest tests/tests.py

Common usage and tips:

With help, you can visualize all possible arguments, which include all user-settable parameters and activation or deactivation of some NERVE components. Definitions and setting options are shown in detail for each of them here above. Important: always specify relative paths for input files and working directory.

Mandatory arguments:

-p1 ,--proteome1
-g , --gram

All the other showed arguments are optional. So, if they're not set by the user, their related default value is used during NERVE computation.

Starting the analysis

To start with NERVE, the -p1,--proteome1 file, which contains all bacterial FASTA proteins to be analyzed, has to be put in the NERVE folder.

./NERVE.sh -p1 anthracis.fasta -g p

Here, the example file "anthracis.fasta", with Gram positive proteins, is saved in the NERVE folder.

But the user can also retrieve a specific proteome from Uniprot, writing its correct ID:

./NERVE.sh -p1 UP000000594 -g p

Here, the reported Uniprot proteome ID is the one of Bacillus anthracis (strain Ames Ancestor).

The next step is the activation/deactivation of facultative components and their parameters settings.

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Facultative components are: Annotation, Loop-Razor, Mouse immunity, NERVirulent, Conservation, Select and Epitope prediction. Only the last two ones are acttivated by default.

</p> See last section for setting examples.

Showing computation

This is an output example, showing the percentage of analysis completion:

 ./NERVE.sh -p

NERVE

Install / Use

README

NERVE

Key features:

Installation procedure of stand-alone version:

Common usage and tips:

Starting the analysis

Showing computation