title: 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.
authors.affiliation: Indiana University School of Informatics, Indiana University-Purdue University and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Haoyu
authors.initials: H
authors.lastname: Cheng
authors.forename: Wai Soon
authors.initials: WS
authors.lastname: Chan
authors.forename: Zhixiu
authors.initials: Z
authors.lastname: Li
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.forename: Song
authors.initials: S
authors.lastname: Liu
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030562:Databases, Protein; D005544:Forecasting; D058977:Molecular Sequence Annotation / Q000379:methods* / Q000639:trends; D016366:Open Reading Frames / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: D003062:Codon; D029701:Saccharomyces cerevisiae Proteins