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Front Immunol. 2013 Dec 4;4:416. doi: 10.3389/fimmu.2013.00416.

A guide to bioinformatics for immunologists.

Author information

  • 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.

Abstract

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; scavenger receptor; sequence alignments; single-nucleotide polymorphisms; transcriptional profiling

PMID:
24363654
[PubMed]
PMCID:
PMC3849744
Free PMC Article

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