New SSU Alignment and Phylogenetic Pipeline: STAP

Ok, here's where I, as the "microbial" person on this blog start speaking another language: most microbiologists, especially those who conduct large-scale environmental sampling for novel lineages of bacteria, archaea, and microbial eukaryotes, still use (gasp!) small subunit ribosomal RNA sequences for identifying organisms and analyzing communities. The reason is simple - primers to amplify these genes are almost completely universal so can be counted on to pick out even rare ("unculturable" almost goes without saying) microbes and, perhaps more importantly, these genes rarely undergo horizontal gene transfer and so are thought to be reliable for identifying truly new bugs out there. The problem has been that the process of taking a slew of these sequences and cranking them through available software to see who was living in your favorite type of sludge was a tedious process involving many different programs. The slowest part of this process was often manual editing of the matrix to adjust alignments. Recently, Wu et al. developed a new pipeline that can completely automate this process, called "Small Subunit rRNA Taxonomy and Alignment Pipeline" or STAP, for short. Although getting this pipeline going requires that you have a basic bioinformatics toolkit installed and compiled (including ClustalW, PhyML and some BioPerl scripts), once this thing is up and running, it is fast (& parallelizable), reliable (more reliable than BLASTN as you approach finer taxonomic scales - see figure above), and open source. Kudos to fellow blogger Jonathan Eisen and his crew for making the lives of Venter-ites everywhere a little easier - and bacterial taxonomy and systematics a lot more solid at the same time.