A guide to bioinformatics for immunologists
- 1Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- 2Department of Biology, McMaster University, Hamilton, ON, Canada
- 3Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
Bioinformatics includes a suite of methods, which are cheap, approachable, and many of which are easily accessible without any sort of specialized bioinformatic training. Yet, despite this, bioinformatic tools are under-utilized by immunologists. Herein, we review a representative set of publicly available, easy-to-use bioinformatic tools using our own research on an under-annotated human gene, SCARA3, as an example. SCARA3 shares an evolutionary relationship with the class A scavenger receptors, but preliminary research showed that it was divergent enough that its function remained unclear. In our quest for more information about this gene – did it share gene sequence similarities to other scavenger receptors? Did it contain conserved protein domains? Where was it expressed in the human body? – we discovered the power and informative potential of publicly available bioinformatic tools designed for the novice in mind, which allowed us to hypothesize on the regulation, structure, and function of this protein. We argue that these tools are largely applicable to many facets of immunology research.
Keywords: bioinformatics, immunology, sequence alignments, single-nucleotide polymorphisms, transcriptional profiling, scavenger receptor
Citation: Whelan FJ, Yap NVL, Surette MG, Golding GB and Bowdish DME (2013) A guide to bioinformatics for immunologists. Front. Immunol. 4:416. doi: 10.3389/fimmu.2013.00416
Received: 10 September 2013; Accepted: 13 November 2013;
Published online: 04 December 2013.
Edited by:Fabrizio Mattei, Istituto Superiore di Sanità, Italy
Reviewed by:Geanncarlo Lugo-Villarino, Centre National de la Recherche Scientifique, France
Can Peng, Tongji University, China
Copyright: © 2013 Whelan, Yap, Surette, Golding and Bowdish. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Dawn M. E. Bowdish, Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada e-mail: firstname.lastname@example.org