Specificity and sensitivity of PROMIR, ERPIN and MIR-ABELA in predicting pre-microRNAs in the chicken genome.
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 5000 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.
Sebastian
Bram
B
Poultry Genetics and Biotechnology Laboratory, Department of Poultry Science, Institute of Bioinformatics, University of Georgia, Athens, GA 30602-2772, USA.
Aggrey
Samuel E
SE
D000818:Animals; D002645:Chickens / Q000235:genetics*; D003198:Computer Simulation; D016678:Genome / Q000235:genetics*; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics*; D012680:Sensitivity and Specificity; D012984:Software
D035683:MicroRNAs