Fig. 1

Molecular background and overview of ExOrthist. a Schematic representation of the exon-intron structure in eukaryotic protein-coding genes and of the molecular events necessary to generate a protein. The DNA is transcribed into pre-mRNA, from which introns are removed through the process of splicing. The exons are joined in the mature mRNA, where each adjacent group of three nucleotides (codon) encodes a different amino acid. Depending on the codon status at the exon-exon junctions, the removed introns are classified as being in phase 0 (complete codons on both sides of the junction) or phase 1 or 2 (split codons across the junction). The mature mRNA is then translated into a protein. b Overview of the ExOrthist pipeline, including inputs, outputs, processes, additional functionalities, and modules. c Schematic representation of species pairwise IPA alignments generated by ExOrthist. Given a query and a target gene, ExOrthist aligns all query gene non-redundant protein isoforms against all target gene non-redundant protein isoforms and introduces the position of each intron respect to the protein-coding sequence as a 0, 1, or 2, depending on its phase. The figure highlights some common scenarios in IPA alignments: exon matches detected in only one of the aligned isoforms, introns with conserved phases, and query exons matching multiple target exons (which will be specifically realigned)