Developing a bioinformatics pipeline for comparative protein classification analysis

Abstract Background Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. Results The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with “population analysis” to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1–11, 2015). Conclusions This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.