Bioinformatics tools and databases focused on genomic islands and secondary metabolite biosynthesis of Streptomyces

Abstract:

With many Streptomyces genomic sequences made available by next generation sequencing (NGS), the bioinformatics resource comes as the answer to an acute demand of the big data mining. In this study, I collected the frequently used tools and open-access databases for genome alignment and island detection, suitable for the large Streptomyces genomes with high G+C content. To illustrate these user-friendly tools, I identified the Actinobacteria integrative and conjugative elements in 12 completely sequenced Streptomyces genomes, which were found to be inserted into the core regions of the Streptomyces chromosomes. The bioinformatics resources currently available for secondary metabolites isolated from Streptomyces species are also described briefly, such as the web-based tool ThioFinder to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach.