aaindex: A Python repository from amckenna41

Python package for working with the AAindex database (https://www.genome.jp/aaindex/)

Introduction
Requirements
Installation
Usage
Tests
Contact
License
References

Introduction

The AAindex is a database of numerical indices representing various physicochemical, structural and biochemical properties of amino acids and pairs of amino acids 🧬. The AAindex consists of three sections: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature [1].

This aaindex Python software package is a very lightweight way of accessing the data represented in the various AAindex databases, requiring no additional external library installations. Any record within the 3 databases and their associated data/numerical indices can be accessed in one simple command. Currently the software supports the AAindex1 database with plans to include the AAindex 2 & 3 in the future.

A demo of the software is available here.

Installation

Install the latest version of aaindex using pip:

pip3 install aaindex --upgrade

Install by cloning the repository:

git clone https://github.com/amckenna41/aaindex.git
python3 setup.py install

Usage

The aaindex package is made up of three modules for each AAindex database, with each having a Python class of the same name, when importing the package you should import the required database module:

from aaindex import aaindex1
# from aaindex import aaindex2
# from aaindex import aaindex3

AAIndex1 Usage

Get record from AAindex1

The AAindex1 class offers diverse functionalities for obtaining any element from any record in the database. The records are imported from a parsed json in the data folder of the package. You can search for a particular record by its record code/accession number or its name/description. You can also get the record category, references, notes, correlation coefficients, PMID and importantly its associated amino acid values:

from aaindex import aaindex1

full_record = aaindex1['CHOP780206']   #get full AAI record
''' full_record ->
{'category': 'sec_struct', 'correlation_coefficients': {}, 
'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)', 'notes': '', 'pmid': '364941', 
'references': "Chou, P.Y. and Fasman, G.D. 'Prediction of the secondary structure of proteins from their amino acid sequence' Adv. Enzymol. 47, 45-148 (1978)", 'values': {'-': 0, 'A': 0.7, 'C': 0.65, 'D': 0.98, 'E': 1.04, 'F': 0.93, 'G': 1.41, 'H': 1.22, 'I': 0.78, 'K': 1.01, 'L': 0.85, 'M': 0.83, 'N': 1.42, 'P': 1.1, 'Q': 0.75, 'R': 0.34, 'S': 1.55, 'T': 1.09, 'V': 0.75, 'W': 0.62, 'Y': 0.99}}
'''

#get individual elements of AAindex record
record_values = aaindex1['CHOP780206']['values'] 
record_values = aaindex1['CHOP780206'].values
#'values': {'-': 0, 'A': 0.7, 'C': 0.65, 'D': 0.98, 'E': 1.04, 'F': 0.93, 'G': 1.41, 'H': 1.22, 'I': 0.78, 'K': 1.01, 'L': 0.85, 'M': 0.83, 'N': 1.42, 'P': 1.1, 'Q': 0.75, 'R': 0.34, 'S': 1.55, 'T': 1.09, 'V': 0.75, 'W': 0.62, 'Y': 0.99}

record_description = aaindex1['CHOP780206']['description']
record_description = aaindex1['CHOP780206'].description
#'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)'

record_references = aaindex1['CHOP780206']['references']
record_references = aaindex1['CHOP780206'].references
#'references': "Chou, P.Y. and Fasman, G.D. 'Prediction of the secondary structure of proteins from their amino acid sequence' Adv. Enzymol. 47, 45-148 (1978)"

record_notes = aaindex1['CHOP780206']['notes']
record_notes = aaindex1['CHOP780206'].notes
#""

record_correlation_coefficient = aaindex1['CHOP780206']['correlation_coefficient']
record_correlation_coefficient = aaindex1['CHOP780206'].correlation_coefficient
#{}

record_pmid = aaindex1['CHOP780206']['pmid']  
record_pmid = aaindex1['CHOP780206'].pmid
#364941

record_category = aaindex1['CHOP780206']['category']
record_category = aaindex1['CHOP780206'].category
#sec_struct

Get total number of AAindex1 records

aaindex1.num_records()

Get list of all AAindex1 record codes

aaindex1.record_codes()

Get list of all AAindex1 record names

aaindex1.record_names()

AAIndex2 Usage

# from aaindex import aaindex1
from aaindex import aaindex2
# from aaindex import aaindex3

AAIndex3 Usage

# from aaindex import aaindex1
# from aaindex import aaindex2
from aaindex import aaindex3

Directories 📁

/tests - unit and integration tests for aaindex package.
/aaindex - source code and all required external data files for package.
/images - images used throughout README.
/docs - aaindex documentation.

Tests 🧪

To run all tests, from the main aaindex folder run:

python3 -m unittest discover tests

Contact ✉️

If you have any questions or comments, please contact amckenna41@qub.ac.uk or raise an issue on the Issues tab.

License

Distributed under the MIT License. See LICENSE for more details.

References

[1]: Shuichi Kawashima, Minoru Kanehisa, AAindex: Amino Acid index database, Nucleic Acids Research, Volume 28, Issue 1, 1 January 2000, Page 374, https://doi.org/10.1093/nar/28.1.374
[2]: https://www.genome.jp/aaindex/

amckenna41/aaindex