Algorithm to address Orthology and Paralogy at the Transcript Level
Project description
Inferring clusters of orthologous and paralogous transcripts
Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach
About The Project
Overview
A graph-based method to infer isoorthology & recent paralogy relations in a set of homologous transcripts
Requirements
python3 (at leat python 3.6)
NetworkX
Pandas
Numpy
ETE toolkit
About the package
install the package
pip3 install transcriptorthology
import package and use the main function
from transcriptorthology.transcriptOrthology import inferring_transcripts_isoorthology
if __name__ == '__main__':
gtot_path = './execution/mapping_gene_to_transcripts/ENSGT00390000003967.fasta'
gt_path = './execution/NHX_trees/ENSGT00390000003967.nhx'
lower_bound = 0.7
transcripts_msa_path = './execution/transcripts_alignments/ENSGT00390000003967.alg'
tsm_value = 1
constraint = 1
output_folder = './execution/output_folder'
inferring_transcripts_isoorthology(transcripts_msa_path, gtot_path, gt_path,tsm_value,lower_bound,constraint,output_folder)
Copyright © 2023 CoBIUS LAB
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