CAMBer

Started with looking for corresponding genes in different bacteria strains to study drug resistance in tuberculosis

Challenges of working with bacteria strains: missing genes in annotation, different TIS in different strains

Objective is to unify the annotations and find 1-1 orthologs

Find transitive closure of BLAST hits in the strains using very stringent criteria. Concept of multigene: one stop codon, multiple TIS. Construct BLAST hit graph (consolidation graph)

Identification of orthlogous groups using anchors. Anchors are 1-1 orthologs. Non-anchors have more than 1 ortholog in a strain. Repeatedly remove edges connecting two non-anchors without anchor support. An edge (pair of genes) has anchor support if it is flanked by two anchors.

Makes use of distance between genes to identify which pair of a tandem duplication is the original one.