Identification of protein coding regions in RNA transcripts

Nucleic Acids Research

Volumn 43, Issue 12, 2015, Pages

  Tang, Shiyuyun ^a   Lomsadze, Alexandre ^a   Borodovsky, Mark ^a,b,c  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Georgia Institute of Technology   (United States)

^c MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

AB INITIO CALCULATION; ACCURACY; ARABIDOPSIS THALIANA; ARTICLE; CLASSIFICATION ALGORITHM; DROSOPHILA MELANOGASTER; GENE IDENTIFICATION; GENEMARKS-T ALGORITHM; GENETIC CODE; MOLECULAR MODEL; MUS MUSCULUS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSCRIPTION; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ALIGNMENT; TRANSLATION INITIATION; ALGORITHM; ANIMAL; ARABIDOPSIS; CHEMISTRY; COMPUTER PROGRAM; GENE; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; MOUSE; OPEN READING FRAME; PROCEDURES; RNA TRANSLATION; SCHIZOSACCHAROMYCES; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; ARABIDOPSIS; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; OPEN READING FRAMES; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RNA, MESSENGER; SCHIZOSACCHAROMYCES; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84942117101     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv227     Document Type: Article

References (56)

1. Garber, M., Grabherr, M.G., Guttman, M. and Trapnell, C. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
2. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
3. Steijger, T., Abril, J.F., Engstrom, P.G, Kokocinski, F., Hubbard, T.J., Guigo, R., Harrow, J., Bertone, P. and RGASP Consortium. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods, 10, 1177-1184.
4. Iseli, C, Jongeneel, C.V. and Bucher, P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol, 99, 138-148.
5. Liu, J.F., Gough, J. and Rost, B. (2006) Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet., 2, 529-536.
6. Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, PD, Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M. et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc, 8, 1494-1512.
7. Besemer, J., Lomsadze, A. and Borodovsky, M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
8. Hyatt, D, Chen, GL., Locascio, PF, Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
9. Delcher, A.L., Bratke, K.A., Powers, E.C. and Salzberg, S.L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679.
10. Kozak, M. (1987) An analysis of 5'-noncoding sequences from 699 vertebrate messenger-RNAs. Nucleic Acids Res., 15, 8125-8148.
11. Ingolia, NT, Ghaemmaghami, S., Newman, J.R.S. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
12. Lee, S., Liu, B.T, Lee, S., Huang, S.X., Shen, B. and Qian, S.B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl. Acad. Sci. U.S.A., 109, E2424-E2432.
13. Besemer, J. and Borodovsky, M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
14. Chen, S.L., Lee, W., Hottes, A.K., Shapiro, L. and McAdams, H.H. (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. U.S.A., 101, 3480-3485.
15. Zhu, W., Lomsadze, A. and Borodovsky, M. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
16. Vivancos, A.P., Guell, M., Dohm, J.C., Serrano, L. and Himmelbauer, H. (2010) Strand-specific deep sequencing of the transcriptome. Genome Res., 20, 989-999.
17. Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
18. Roberts, A., Pimentel, H., Trapnell, C. and Pachter, L. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27, 2325-2329.
19. Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S. and Morgenstern, B. (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res., 34, W435-W439.
20. Zerbino, D.R. and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
21. Schulz, M.H., Zerbino, D.R., Vingron, M. and Birney, E. (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28, 1086-1092.
22. Slater, G.S. and Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
23. Ingolia, N.T., Lareau, L.F. and Weissman, J.S. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
24. Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F., Schreiber, S., Platzer, M., Krawczak, M., Hampe, J. et al. (2012) Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res., 22, 2208-2218.
25. Gerashchenko, M.V. and Gladyshev, V.N. (2015) Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res., 42, e134.
26. Antonov, I., Coakley, A., Atkins, J.F., Baranov, P.V. and Borodovsky, M. (2013) Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res., 41, 6514-6530.
27. Tang, S., Antonov, I. and Borodovsky, M. (2013) MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinformatics, 29, 114-116.
28. Antonov, I. and Borodovsky, M. (2010) Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J. Bioinform. Comput. Biol., 8, 535-551.
29. Garber, M., Grabherr, M.G., Guttman, M. and Trapnell, C. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
30. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
31. Steijger, T., Abril, J.F., Engstrom, P.G, Kokocinski, F., Hubbard, T.J., Guigo, R., Harrow, J., Bertone, P. and RGASP Consortium. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods, 10, 1177-1184.
32. Iseli, C, Jongeneel, C.V. and Bucher, P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol, 99, 138-148.
33. Liu, J.F., Gough, J. and Rost, B. (2006) Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet., 2, 529-536.
34. Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, PD, Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M. et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc, 8, 1494-1512.
35. Besemer, J., Lomsadze, A. and Borodovsky, M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
36. Hyatt, D, Chen, GL., Locascio, PF, Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
37. Delcher, A.L., Bratke, K.A., Powers, E.C. and Salzberg, S.L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679.
38. Kozak, M. (1987) An analysis of 5'-noncoding sequences from 699 vertebrate messenger-RNAs. Nucleic Acids Res., 15, 8125-8148.
39. Ingolia, NT, Ghaemmaghami, S., Newman, J.R.S. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
40. Lee, S., Liu, B.T, Lee, S., Huang, S.X., Shen, B. and Qian, S.B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl. Acad. Sci. U.S.A., 109, E2424-E2432.
41. Besemer, J. and Borodovsky, M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
42. Chen, S.L., Lee, W., Hottes, A.K., Shapiro, L. and McAdams, H.H. (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. U.S.A., 101, 3480-3485.
43. Zhu, W., Lomsadze, A. and Borodovsky, M. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
44. Vivancos, A.P., Guell, M., Dohm, J.C., Serrano, L. and Himmelbauer, H. (2010) Strand-specific deep sequencing of the transcriptome. Genome Res., 20, 989-999.
45. Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
46. Roberts, A., Pimentel, H., Trapnell, C. and Pachter, L. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27, 2325-2329.
47. Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S. and Morgenstern, B. (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res., 34, W435-W439.
48. Zerbino, D.R. and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
49. Schulz, M.H., Zerbino, D.R., Vingron, M. and Birney, E. (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28, 1086-1092.
50. Slater, G.S. and Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
51. Ingolia, N.T., Lareau, L.F. and Weissman, J.S. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
52. Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F., Schreiber, S., Platzer, M., Krawczak, M., Hampe, J. et al. (2012) Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res., 22, 2208-2218.
53. Gerashchenko, M.V. and Gladyshev, V.N. (2015) Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res., 42, e134.
54. Antonov, I., Coakley, A., Atkins, J.F., Baranov, P.V. and Borodovsky, M. (2013) Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res., 41, 6514-6530.
55. Tang, S., Antonov, I. and Borodovsky, M. (2013) MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinformatics, 29, 114-116.
56. Antonov, I. and Borodovsky, M. (2010) Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J. Bioinform. Comput. Biol., 8, 535-551.