Designing a dedicated database for eukaryotic algae species — A case study on cross-species comparison of P450 enzymes

Public molecular sequences and structures for animal and plant species are growing rapidly. It frequently leads to the retrieving results of homologous search containing undesirable entries from different organisms. To reduce unwanted output, a dedicated database for performing genomic comparison on a specific organism is required. In this study, a set of suitable bioinformatics tools and a comprehensive database are designed and integrated for comparative analyses among eukaryotic algae species. Through cross-species comparison, the proposed system is able to retrieve homologous protein sequences and structures from collected algae species only. A matching technique based on secondary structure characteristics are designed for retrieving and aligning remote sequences in an efficient and effective approach. It is especially helpful and superior for protein sequences possessing low similarities and without any resolved structural information. To demonstrate the effective searching results, the homologous searching and keyword analysis for Cytochrome CYP450 enzymes is illustrated as an example to emphasize the importance of structural feature conservation among remote homologous organisms and to exploit the advantages of such characteristics for remote protein matching among algae species.