PyCanal: A Python package for conservation analysis of homologous protein sequences

PyCanal is a python tool for evaluating amino acid conservation in sites of homologous proteins. Homologous proteins may be obtained via tools such as BLAST, HMM, etc. PyCanal takes as input a multiple sequence alignment of homologous proteins in fasta format, and then calculates conservation scores for each site in a reference sequence chosen by the user from the alignment.

Installation

Download from GitHub and install:

git clone https://github.com/jafetgado/pycanal.git
cd pycanal
python setup.py install

Examples

An example showing how to compute conservation scores with PyCanal for 1,748 sequences of glycoside hydrolase family 7.

from pycanal import Canal

# Create an instance of the Canal class
canal = Canal(fastafile='example/alignment.fasta', #Multiple sequence alignment (MSA) of homologous sequences
              ref=0, #Position of reference sequence in MSA, use first sequence
              startcount=-16, #Position label of first residue in reference sequence
              verbose=True # Print out progress
              )

# Compute conservation scores for each site in reference sequence with relative entropy method
cons_scores = canal.analysis(include=None, method='relative')

# Plot the distribution of amino acids in at position 77 and save image as position77.png
canal.plotSiteDistribution(site=77, saveplot='position77')

# Determine consensus sequence from the alignment and save as fasta file
consensus_sequence = canal.getConsensusSequence(savefasta='consensus_sequence.fasta')

Amino acid distribution at position 77

Relative entropy conservation scores

Citation

If you find PyCanal useful, please cite:

Gado, Japheth E., 2021, "Machine learning and bioinformatic insights into key enzymes for a bio-based circular economy". Theses and Dissertations: Chemical and Materials Engineering, 129. DOI: 10.13023/etd.2021.009.