- Communication -

Volume 8

Full article

Specificity and sensitivity of PROMIR, ERPIN and MIR-ABELA in predicting pre-microRNAs in the chicken genome

Bram Sebastian and Samuel E. Aggrey*

Poultry Genetics and Biotechnology Laboratory, Department of Poultry Science and
Institute of Bioinformatics, University of Georgia, Athens, GA 30602-2772, USA

* Corresponding authors
   Email: saggrey@uga.edu



Edited by E. Wingender; received April 02, 2008; revised and accepted July 22, 2008; published August 02, 2008

Abstract

MicroRNAs (miRNAs) are endogenous 21-23 nucleotide molecules that are known to regulate about 30% of protein-coding genes through the RNAi pathway. Low level expression of some miRNA has limited their in-situ discovery. Such limitations could be ameliorated by in-silico methodologies. The efficacies of three major programs (ERPIN, ProMir and miR-abela) in detecting known pre-miRNA were evaluated using chicken pre-miRNA data. The sensitivity of ProMir, miR-abela and ERPIN were 53%, 57% and 93%, respectively. The specificity of the three algorithms using 5,000 random sequences was 98.94%, 99.46%, and 99.10% for ProMir-g, ERPIN and miR-abela, respectively. The sensitivities of the existing programs are low for chicken data and an efficient algorithm may be needed to predict novel chicken pre-miRNAs.

Keywords: microRNA, ProMir-g, ERPIN, miR-abela, sensitivity, specificity