Workflow of the Bagheera web application. A) Upon uploading of the yeast genome or transcriptome assembly data homologous proteins to the reference sequences are identified using TBLASTN and subsequently predicted by AUGUSTUS-PPX. The reference sequences used for the gene prediction are selected according to the species selected as model organism for AUGUSTUS. The predicted proteins are aligned to the reference alignments (NW = Needleman-Wunsch, SW = Swith-Waterman, LCS = Longest Common Subsequence) and the codon usage predicted based on the analysis of sequence similarity and CUG codon conservation at CUG codon positions. Optionally, a phylogenetic tree can be calculated based on a randomly selected and concatenated subset of the predicted proteins. B) A gene reconstruction of the uploaded protein sequence is performed to obtain cDNA sequence. The species encoding the uploaded protein has to be specified. The cDNA sequence is then translated according to the translation scheme of the respective species.