lucodevro / comparative-genomics-of-gloeobacter-and-theobroma

Identifying orthologs, paralogs and co-orthologs using BBH, phylogenetic tree analysis using ClustalW and conservation assessment using a simplified Valdar metric

Comparative-Genomics-of-Gloeobacter-and-Theobroma

Code and limited results repository for the assignment for the course Comparative genomics, MSc of Bioinformatics, KU Leuven, 2023

Contents:

• BLAST both organisms against each other (blast_both_all.pds)
• Find BBHs for ortholog, paralog and co-ortholog detection (bbh.py)
• BLAST a Gloeobacter proteins against 25 handpicked proteomes to find all homologs (get_homologs.pbs)
• Parse results and identify homologs (homologs.py)
• Create a simple NJ phylogenetic tree using ClustalW (homologs.phb)
• Assess conservation across regions (conservation.py)