title: A method for identification of selenoprotein genes in archaeal genomes.
abstract: The genetic codon UGA has a dual function: serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should be a real selenoprotein gene. The result shows that Asec-Prediction is effective for the prediction of archaeal selenoprotein genes.
authors: Department of Physics, Huazhong University of Science and Technology, Wuhan, China.
authors: Mingfeng
authors: M
authors: Li
authors: Yanzhao
authors: Y
authors: Huang
authors: Yi
authors: Y
authors: Xiao
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000235:genetics*; D020745:Genome, Archaeal; D023281:Genomics / Q000379:methods*; D017020:Methanosarcina / Q000235:genetics; D008969:Molecular Sequence Data; D051140:Selenoproteins / Q000032:analysis / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D051140:Selenoproteins