Work

Identification of protein coding regions in RNA transcripts

Year: 2015

Type: article

Abstract: Massive parallel sequencing of RNA transcripts by next-generation technology (RNA-Seq) generates critically important data for eukaryotic gene discovery. Gene finding in transcripts can be done by statistical (alignment-free) as well as by alignment-based methods. We describe a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. The algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. We demonstrate that (i) the unsupervised training is robust with respect to the presence of transcripts assembly errors and (ii) the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting translation initiation sites in modelled as well as in assembled transcripts compares favourably to other existing methods.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkv227

Authors: Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky

Institutions: Georgia Institute of Technology, The Wallace H. Coulter Department of Biomedical Engineering, Moscow Institute of Physics and Technology

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: University of Oxford, National Institutes of Health, National Human Genome Research Institute