Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families

Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on any specific member of that said family. This step is often performed only superficially or partially by experimentalists as the most common approaches and tools to pursue this objective are far from optimal. Using a previously gathered dataset of 284 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3), we evaluated the productivity of different databases and search tools, and devised a workflow that can be used by experimentalists to capture the most information in less time. To complement this workflow, web-based platforms allowing for the exploration of member distributions for several protein families across sequenced genomes or for the capture of gene neighborhood information were reviewed for their versatility, completeness and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.