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bio2Byte software suite to predict protein biophysical properties from their amino-acid sequences

Project description


Bio2Byte Tools

This package provides you structural predictions for protein sequences made by Bio2Byte group.

       

🧪 List of available predictors

Predictor Usage
Dynamine Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle.
Disomine Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding.
EfoldMine Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events.
AgMata Single-sequence based predictor of protein regions that are likely to cause beta-aggregation.
PSPer PSP (Phase Separating Protein) predicts whether a protein is likely to phase-separate with a particular mechanism involving RNA interacts (FUS-like proteins). It will highlight the regions in your protein that are involved mechanistically, and provide an overall score.

🔗 Related link: These listed tools and others are described on the Bio2Byte website inside the Tools section.

⚡️Quick start

First of all, download and install the package:

$ pip install b2bTools

Single Sequence predictions

Use this example as an entry point:

import matplotlib.pyplot as plt
from b2bTools import SingleSeq

single_seq = SingleSeq("/path/to/example.fasta")
single_seq.predict(tools=['dynamine', 'agmata'])
predictions = single_seq.get_all_predictions('SEQ001')

backbone_pred = predictions['SEQ001']['backbone']
sidechain_pred = predictions['SEQ001']['sidechain']
agmata_pred = predictions['SEQ001']['agmata']

plt.plot(range(len(backbone_pred)), backbone_pred, label = "Backbone")
plt.plot(range(len(backbone_pred)), sidechain_pred, label = "Sidechain")
plt.plot(range(len(backbone_pred)), agmata_pred, label = "Agmata")

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()

There is a live demo available on Google Colab: link

Multiple Sequences Alignment predictions

Use the following example as an entry point. Keep in mind the available tools to run are 'agmata', 'eFoldMine', 'disoMine' (case sensitive) on top of the default one which is Dynamine.

import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_aligned_file("/path/to/example.fasta")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()

In case you need to run another tool, replace the 4th line with:

msaSeq.from_aligned_file("/path/to/example.fasta", tools=['agmata', 'eFoldMine', 'disoMine'])

There is a live demo available on Google Colab: link

⚙️ First time setup

The following steps are required in order to install the b2bTools package in your local environment:

📦 Pip package installation

From the official documentation:

pip is the package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.

🔗 Related link: Pip official documentation.

$ pip install b2bTools

💡 Relevant idea: Using the package from Jupyter Notebooks is a good idea to test the package. If you are using Google Colab, install the package directly from pip inside a code block:

!pip install b2bTools

Important notes for MSA analysis

The PyPI repository does not contains a package for t_coffee which is a dependency to run predictions on MSA when using Blast, UniRed ID, among others. Despite this situation, there is a workaround installing this dependency from conda:

conda install -c bioconda t-coffee

📦 Conda package installation

Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.

🔗 Related link: Conda official documentation.

To install this package with conda, run:

$ conda install -c Bio2Byte b2bTools

⚠️ Important note: some Linux users might experience dependency conflicts during the conda installation. Please use the pip installation (described below) if you encounter them.

If you must use conda, use the following command:

$ conda install --override-channels --channel defaults --channel conda-forge --channel Bio2Byte --channel pytorch b2btools

🐳 Docker-way to quick start

Docker is an open platform for developing, shipping, and running applications. Docker enables you to separate your applications from your infrastructure so you can deliver software quickly. With Docker, you can manage your infrastructure in the same ways you manage your applications. By taking advantage of Docker’s methodologies for shipping, testing, and deploying code quickly, you can significantly reduce the delay between writing code and running it in production.

🔗 Related link: Docker official documentation.

Preconditions

For the moment, Windows users can only use this Docker image using the Windows Linux sub-system feature.

Steps

In order to import/export files from your host to the container and viceversa create a volume using the -v $(pwd)/swap:/data parameter.

⚠️ Important note: Be sure your input files are inside $(pwd)/swap.

$ docker pull diazadriang/b2b-tools-public
$ docker run -it -v $(pwd)/swap:/data diazadriang/b2b-tools-public -disomine -file /data/input_example.fasta -output /data/result.json -identifier test

⚠️ Important note:

  • The output file titled result.json will be stored inshde $(pwd)/swap.
  • The available parameters after diazadriang/b2b-tools-public are:
Parameter Purpose Example
-file Path to the input file -input /path/to/input/file.fasta
-output Path to the output file (a JSON file with the results) -output /path/to/output/results.json
-dynamine Run Dynamine predictor -dynamine
-disomine Run Disomine predictor -disomine
-efoldmine Run EfoldMine predictor -efoldmine
-agmata Run AgMata predictor -agmata
-psp Run PSPer predictor -psp

🐍 Package content

🔧 General Tools

Besides the prediction tools, this package includes general bioinformatics tools useful to manipulate files.

Single Sequences files

The class FastaIO provides the following static methods:

  • read_fasta_from_file
  • read_fasta_from_string
  • write_fasta

Usage:

from b2bTools.general.parsers.fasta import FastaIO

Multiple Sequences Alignments files

The class AlignmentsIO provides the following static methods:

  • read_alignments
  • read_alignments_fasta
  • read_alignments_A3M
  • read_alignments_blast
  • read_alignments_balibase
  • read_alignments_clustal
  • read_alignments_psi
  • read_alignments_phylip
  • read_alignments_stockholm
  • write_fasta_from_alignment
  • write_fasta_from_seq_alignment_dict
  • json_preds_to_csv_singleseq
  • json_preds_to_csv_msa

Usage:

from b2bTools.general.parsers.alignments import AlignmentsIO

NEF files

The class NefIO provides the following static methods:

  • read_nef_file
  • read_nef_file_sequence_shifts

Usage:

from b2bTools.general.parsers.alignments import AlignmentsIO

NMR-STAR files

The class NMRStarIO provides the following static methods:

  • read_nmr_star_project
  • read_nmr_star_sequence_shifts

Usage:

from b2bTools.general.parsers.nmr_star import NMRStarIO

🔍 About predictors

Given a predictor could be built on top of other, it is usual to get more output predictions than the expected:

Predictor Depends on
Dynamine None
EfoldMine [Dynamine]
Disomine [EfoldMine, Dynamine]
AgMata [EfoldMine, Dynamine]

🔬 Single Sequence

🧭 Basic flow

This section will explain you in details the script mentioned inside the Quick start section.

  1. Import the SingleSeq class from the b2bTools package:
from b2bTools import SingleSeq
  1. Instantiate an object by passing the path to the input file in FASTA format:
single_seq = SingleSeq("/path/to/example.fasta")
  1. Run the predictions you want to:
single_seq.predict(tools=['dynamine', 'efoldmine'])

⚠️ Important note: These are all the available options to use inside the tools array parameter:

Predictor string value
Dynamine "dynamine"
EfoldMine "efoldmine"
Disomine "disomine"
AgMata "agmata"
  1. Get the prediction values after running the selected predictors for a specific sequence identifier:
predictions = single_seq.get_all_predictions('SEQ001')

⚠️ Important note: The method get_all_predictions will return a dictionary with the following structure:

{
  "SEQUENCE_ID_000": {
    "seq": "the input sequence 0",
    "result001": [0.001, 0.002, ..., 0.00],
    "result002": [0.001, 0.002, ..., 0.00],
    "...": [...],
    "resultN": [0.001, 0.002, ..., 0.00]
  },
  "SEQUENCE_ID_001": {
    "seq": "the input sequence 1",
    "result001": [0.001, 0.002, ..., 0.00],
    "result002": [0.001, 0.002, ..., 0.00],
    "...": [...],
    "resultN": [0.001, 0.002, ..., 0.00]
  },
  "...": { ... },
  "SEQUENCE_ID_N": {
    "seq": "the input sequence N",
    "result001": [0.001, 0.002, ..., 0.00],
    "result002": [0.001, 0.002, ..., 0.00],
    "...": [...],
    "resultN": [0.001, 0.002, ..., 0.00]
  },
}

To know all the available result keys, please review this table:

Predictor Output key Output values (type) Output values (example)
None "seq" [Char] ['M', 'A', ..., 'S', 'T']
Dynamine "backbone" [Float] [0.6786, 0.71, ..., 0.7219]
Dynamine "sidechain" [Float] [0.5823, 0.23, ..., 0.1995]
Dynamine "helix" [Float] [0.0122, 0.84, ..., 0.2345]
Dynamine "ppII" [Float] [0.0420, 0.69, ..., 0.5566]
Dynamine "coil" [Float] [0.6666, 0.13, ..., 0.9954]
Dynamine "sheet" [Float] [0.1992, 0.12, ..., 0.0020]
EfoldMine "earlyFolding" [Float] [0.1989, 0.08, ..., 0.0031]
Disomine "disoMine" [Float] [0.1996, 0.12, ..., 0.0019]
AgMata "agmata" [Float] [0.1954, 0.06, ..., 0.0007]
  1. You are ready to use the sequence and predictions to work with them. Here is an example of plotting the data.
backbone_pred = predictions['SEQ001']['backbone']
sidechain_pred = predictions['SEQ001']['sidechain']
agmata_pred = predictions['SEQ001']['agmata']

plt.plot(range(len(backbone_pred)), backbone_pred, label = "Backbone")
plt.plot(range(len(backbone_pred)), sidechain_pred, label = "Sidechain")
plt.plot(range(len(backbone_pred)), agmata_pred, label = "Agmata")

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()

⌨️ Running as Python module (no Python code involved)

You are able to use this package directly from your console session with no Python code involved. Further details available on the official Python documentation site

$ python -m b2bTools -file ./swap/input_example.fasta -dynamics -disomine -identifier test -output ./swap/result-from-package.json

⚠️ Important note:

  • The output file titled result.json will be stored inshde $(pwd)/swap.
  • The available parameters after b2b-tools are:
Parameter Purpose Example
-file Path to the input file -input /path/to/input/file.fasta
-output Path to the output file (a JSON file with the results) -output /path/to/output/results.json
-dynamine Run Dynamine predictor -dynamine
-disomine Run Disomine predictor -disomine
-efoldmine Run EfoldMine predictor -efoldmine
-agmata Run AgMata predictor -agmata

🔬 Multiple Sequences Alignment

If your input data is a MSA file, there are many ways to predict the biophysical features of the sequences.

🧭 Basic flow

⚠️ Important note: These are all the available options to use inside the tools array parameter (Dynamine runs always):

Predictor string value
EfoldMine "eFoldMine"
Disomine "eFoldMine"
AgMata "agmata"

The tools array parameter is available for all the input methods of the class MultipleSeq:

# From an aligned file
msaSeq = MultipleSeq()
msaSeq.from_aligned_file("/path/to/example.fasta", tools=['agmata', 'eFoldMine', 'disoMine'])

# From two MSA files
msaSeq = MultipleSeq()
msaSeq.from_two_msa("/path/to/example_a.fasta", "/path/to/example_b.fasta", tools=['agmata', 'eFoldMine', 'disoMine'])

# From a JSON with variations file
msaSeq = MultipleSeq()
msaSeq.from_json("/path/to/example.json", tools=['agmata', 'eFoldMine', 'disoMine'])

# From a sequence performing a BLAST before running the predictions
msaSeq = MultipleSeq()
msaSeq.from_blast("path/to/example.fasta", mut_option="y", mut_position=1, mut_residue="A", tools=['agmata', 'eFoldMine', 'disoMine'])

# From an UniRef ID performing a BLAST before running the predictions
msaSeq = MultipleSeq()
msaSeq.from_uniref("A2R2V4", tools=['agmata', 'eFoldMine', 'disoMine'])

To know all the available result keys, please review this table:

Predictor Output key Output values (type) Output values (example)
Dynamine "backbone" [Float] [0.6786, 0.123, ..., 0.2523]
Dynamine "sidechain" [Float] [0.1234, 0.532, ..., 0.8764]
Dynamine "helix" [Float] [0.4321, 0.425, ..., 0.8334]
Dynamine "ppII" [Float] [0.4577, 0.754, ..., 0.2343]
Dynamine "coil" [Float] [0.5464, 0.675, ..., 0.6483]
Dynamine "sheet" [Float] [0.1234, 0.432, ..., 0.8764]
EfoldMine "earlyFolding" [Float] [0.3245, 0.234, ..., 0.2348]
Disomine "disoMine" [Float] [0.4576, 0.235, ..., 0.6347]
AgMata "agmata" [Float] [0.4323, 0.457, ..., 0.2372]
From an aligned file
import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_aligned_file("/path/to/example.fasta")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()
From two MSA files
import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_two_msa("/path/to/example_a.fasta", "/path/to/example_b.fasta")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()
From a JSON with variations file

In this case, we support a JSON format to introduce variants in a sequence. For instance:

{
  "metadata": { "name": "target_fasta_file" },
  "WT": "MAKSTILALLALVLVAHASAMRRERGRQGDSSSCERQVDRVNLKPCEQHIMQRIMGEQEQYDSYDIRSTRSSDQQQRCCDELNEMENTQRCMCEALQQIMENQCDRLQDRQMVQQFKRELMNLPQQCNFRAPQRCDLDVSGGRC",
  "Variants": {
    "Var1": ["A3S", "A11G"],
    "Var2": ["A2G", "K3_S4insPH", "T5del"]
  }
}

Where WT is the wild-type sequence, and the Variants key includes a dictionary of different variations. Each of them are handled by an array of replacements:

  • <Target Residue><New Residue> (For example: Replace the A at the position 3 with a S would be "A3S")

Regarding the input fasta file, the metadata key contains the name of the input, remember it should stored in the same directory than the json file.

The code snippet is:

import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_json("/path/to/example.json")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()
From a sequence performing a BLAST before running the predictions

In case you want to perform a mutation of a residue at one specific position, you have the parameters mut_position, mut_residue and the value of mut_option must be "y".

import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_blast("path/to/example.fasta", mut_option="y", mut_position=1, mut_residue="A")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()
From an UniRef ID performing a BLAST before running the predictions
import matplotlib.pyplot as plt
from b2bTools import MultipleSeq

msaSeq = MultipleSeq()
msaSeq.from_uniref("A2R2V4")

predictions = msaSeq.get_all_predictions_msa("SEQ001")
backbone_pred = predictions['backbone']
sidechain_pred = predictions['sidechain']

plt.legend()
plt.xlabel('aa_position')
plt.ylabel('pred_values')
plt.show()

⚠️ Note: the query using the UniRef ID was limited to 25 results to increase the time performance.

📚 Package classes & methods

If you are interested in further details, please read the full documentation on the Bio2Byte website.

To generate locally the documentation you can follow the next steps described in this section.

Preconditions

You have downloaded the source code of the Bio2Byte Tools in your local environment:

$ git clone git@bitbucket.org:bio2byte/b2btools.git && cd b2btools

Steps

  1. Run the following command:
$ make generate-docs
  1. And then open folder ./wrapped_documentation

💡 Relevant idea: At any moment, you can read the docs of a method invoking the __doc__ method (e.g. print(SingleSeq.predict.__doc__)).

📖 How to cite

If you use this package or data in this package, please cite:

Predictor Cite Digital Object Identifier (DOI)
Dynamine Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, and Wim Vranken. From protein sequence to dynamics and disorder with DynaMine Nature Communications 4:2741 (2013) https://www.nature.com/articles/ncomms3741
Disomine Gabriele Orlando, Daniele Raimondi, Francesco Codice, Francesco Tabaro, Wim Vranken. Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. bioRxiv 2020.05.25.115253 (2020) https://www.biorxiv.org/content/10.1101/2020.05.25.115253v1
EfoldMine Raimondi, D., Orlando, G., Pancsa, R. et al. Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins. Sci Rep 7, 8826 (2017) https://doi.org/10.1038/s41598-017-08366-3
AgMata Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim Vranken. Accurate prediction of protein beta-aggregation with generalized statistical potentials Bioinformatics , Volume 36, Issue 7, 1 April 2020, Pages 2076–2081 (2020) https://academic.oup.com/bioinformatics/article/36/7/2076/5670527

📝 Terms of use

  1. The Bio2Byte group aims to promote open science by providing freely available online services, database and software relating to the life sciences, with focus on proteins. Where we present scientific data generated by others we impose no additional restriction on the use of the contributed data than those provided by the data owner.
  2. The Bio2Byte group expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated in 'How to cite' sections (or equivalent).
  3. The Bio2Byte group is not liable to you or third parties claiming through you, for any loss or damage.
  4. Any questions or comments concerning these Terms of Use can be addressed to Wim Vranken.

© Wim Vranken, Bio2Byte group, VUB

https://bio2byte.be/b2btools/

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