SeqRank project

The ‘SeqRank’ project aims are to develop approaches for automatic selection of high-quality molecular sequences for microbial strains, through the use of modern ranking techniques. Currently, the SeqRank algorithm can automate the process of selecting a high-quality 16S rRNA gene sequence for any given prokaryotic strain, based on a series of quality statistics, the latest status of taxonomy and the latest sequence information from the INSDC databases. The extended SeqRank workflow applies SeqRank to all type strains of a given prokaryotic genus or family, adds an automatically chosen outgroup sequence, and infers a phylogenetic tree from the resulting list of sequences.

Contact: Wim.DeSmet@UGent.be or the StrainInfo team (see contact)

How do I use it?

Any strain passport includes a link to the SeqRank page for that strain, which will list available 16S rRNA gene sequences for that strain and allows export of the sequences (as well as linking to the relevant passport pages for strain and sequence information). The extended workflow can be launched from any species, genus or family passport, for instance that of Acetobacter, by clicking the SeqRank logo.

The extended SeqRank workflow searches StrainInfo for taxon, strain and sequence information, and is organised in several workflow steps, each of which is represented by a main block in the workflow. Clicking a completed task will show all intermediary data fetched, as well as sometimes allow you to make changes or download data. There are download links provided with results, and drilling down into the history of strains and sequences can be done by visiting the relevant passport pages on StrainInfo, which also link back to their source data providers.