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

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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)

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