Identification of protein coding regions in RNA transcripts. Issue 12 (13th April 2015)

• Record Type: Journal Article
• Authors: Tang, Shiyuyun; Lomsadze, Alexandre; Borodovsky, Mark
• Is Part Of: Nucleic acids research. Volume 43:Issue 12(2015)
• Page Start: e78
• Page End: e78
• Publication Date: 2015-04-13
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkv227
• Languages: English
• ISSNs: 0305-1048

Abstract

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.