Rabifier2: an improved bioinformatic classifier of Rab GTPases

Abstract

Summary: The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases. It is more accurate, significantly faster than the original version and is now open source, both the code and the data, allowing for community participation.

Availability and implementation: Rabifier and RabDB are freely available through the web at http://rabdb.org . The Rabifier package can be downloaded from the Python Package Index at https://pypi.python.org/pypi/rabifier , the source code is available at Github https://github.com/evocell/rabifier .

Contact: jsurkont@igc.gulbenkian.pt or jleal@igc.gulbenkian.pt.

Supplementary information: Supplementary data are available at Bioinformatics online.