Mini-Review

Archives of Microbiology

, Volume 192, Issue 3, pp 151-155

An overview of in silico protein function prediction

  • Roy D. SleatorAffiliated withDepartment of Biological Sciences, Cork Institute of TechnologyCIT Bioinformatics Group, Cork Institute of Technology Email author 
  • , Paul WalshAffiliated withDepartment of Computing, Cork Institute of TechnologyCIT Bioinformatics Group, Cork Institute of Technology

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Abstract

As the protein databases continue to expand at an exponential rate, fed by daily uploads from multiple large scale genomic and metagenomic projects, the problem of assigning a function to each new protein has become the focus of significant research interest in recent times. Herein, we review the most recent advances in the field of automated function prediction (AFP). We begin by defining what is meant by biological “function” and the means of describing such functions using standardised machine readable ontologies. We then focus on the various function-prediction programs available, both sequence and structure based, and outline their associated strengths and weaknesses. Finally, we conclude with a brief overview of the future challenges and outstanding questions in the field, which still remain unanswered.

Keywords

Protein function Homology-based transfer Ontologies Sequence and structure Motifs