eprintid: 1550420
rev_number: 49
eprint_status: archive
userid: 608
dir: disk0/01/55/04/20
datestamp: 2017-04-15 21:24:33
lastmod: 2020-05-31 08:48:47
status_changed: 2017-07-17 13:26:17
type: article
metadata_visibility: show
creators_name: Surkont, J
creators_name: Diekmann, Y
creators_name: Pereira-Leal, JB
title: Rabifier2: an improved bioinformatic classifier of Rab GTPases
ispublished: pub
divisions: UCL
divisions: A01
divisions: B02
divisions: C08
note: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
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.
date: 2017-02-15
date_type: published
publisher: OXFORD UNIV PRESS
official_url: https://doi.org/10.1093/bioinformatics/btw654
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
article_type_text: Article
verified: verified_manual
elements_id: 1285858
doi: 10.1093/bioinformatics/btw654
lyricists_name: Diekmann, Yoan
lyricists_id: YDIEK55
actors_name: Flynn, Bernadette
actors_id: BFFLY94
actors_role: owner
full_text_status: public
publication: Bioinformatics
volume: 33
number: 4
pagerange: 568-570
pages: 3
issn: 1460-2059
citation:        Surkont, J;    Diekmann, Y;    Pereira-Leal, JB;      (2017)    Rabifier2: an improved bioinformatic classifier of Rab GTPases.                   Bioinformatics , 33  (4)   pp. 568-570.    10.1093/bioinformatics/btw654 <https://doi.org/10.1093/bioinformatics%2Fbtw654>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/1550420/1/Surkont_Rabifier2_improved_bioinformatic.pdf