Bioinf-PHP: Bioinformatics Pipeline for Protein Homology and Phylogeny.

Catalase is a special category of enzyme that plays a critical role in regulating the level of harmful hydrogen peroxide in cells. There are three main families of these proteins: Typical Catalases, Catalase-Peroxidases (katG), and Manganese Catalases. In order to uncover potential evolutionary relationships between these enzymes, we have developed a bioinformatics pipeline named Bioinf-PHP to search for protein homology and phylogeny, and to compare these three families at the functional level based on sequence similarity. Protein motif analysis of the sequences featured in the pipeline were conducted using the MEME algorithm. The top three significant motifs were reported for all of the catalase sequences. The Bioinf-PHP pipeline also runs BLASTP to search for homology between bacteria catalase and yeast protein sequences. The neighbor-joining phylogenetic tree was constructed with Saccharomyces cerevisiae to infer evolutionary relationships as a test example. The structural similarities between orthologous sequences provided further evidence of functional similarity.