Small open reading frames: current prediction techniques and future prospect

Abstract

Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio techniques. It highlights the urgent need for both experimental and computational studies in order to further advance the accuracy of sORF prediction.

Fig. (1)

Significant drop in performance is observed for the popular homolog-search technique BLAST (in Red) and ab initio predictor codonW (in Blue). The receiver operating curves are shown for the best performed BLAST search in NR database for sORFs (excluding 50% or more homologous sequences) and for ORFs with 100–150 codons (excluding 70% or more homologous sequence) along with the performance of codonW for sORFs and ORFs with 100–150 codons, respectively.

Fig. (2)

As in Fig.1 but for sORF only with an additional method called sORF finder (in Black).