RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Yuan, Cheng ^a   Sun, Yanni ^a  

^a Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC PROCEDURES; GENOME; METAGENOMICS; NEXT GENERATION SEQUENCING DATA; RNA ANALYSIS; RNA CODE; RNA SEQUENCE; RNA TRANSLATION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE;

ARABIDOPSIS; GENOME; HUMANS; METAGENOMICS; RNA, RIBOSOMAL, 16S; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 84886422310     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0077596     Document Type: Article

References (26)

1. Jones-Rhoades MWW, Bartel DPP, Bartel B, (2006) MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 57: 19-53.
2. Lu S, Shi R, Tsao CC, Yi X, Li L, et al. (2004) RNA silencing in plants by the expression of siRNA duplexes. Nucleic acids research 32: e171-e171.
3. Eddy SR, (2001) Non-coding RNA genes and the modern RNA world. Nature Reviews Genetics 2: 919-929.
4. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, et al. (2011) Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12s/16s/18s) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie Van Leeuwenhoek 100: 471-475.
5. Shah N, Tang H, Doak TG, Ye Y (2011) Comparing bacterial communities inferred from 16s rRna gene sequencing and shotgun metagenomics. In: Pacific Symposium on Biocomputing. World Scientific, volume 16, pp.165-176.
6. Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF, et al. (2011) EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol 12: R44.
7. Fan L, McElroy K, Thomas T, (2012) Reconstruction of ribosomal RNA genes from metagenomic data. PLoS One 7: e39948.
8. Stricklin Sea (2005) C. elegans noncoding RNA genes, WormBook, ed. The C. elegans Research Community. WormBook.
9. Ge X, Zhang Y, Jiang J, Zhong Y, Yang X, et al. (2013) Identification of MicroRNAs in Helicoverpa armigera and Spodoptera litura based on deep sequencing and homology analysis. Int J Biol Sci 9: 1-15.
10. Gruber AR, Neuböck R, Hofacker IL, Washietl S, (2007) The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Research 35: W335-W338.
11. Nawrocki EP, Kolbe DL, Eddy SR, (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335-1337.
12. Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 0955-964.
13. Lowe TM, Eddy SR, (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168-1171.
14. Kolbe DL, Eddy SR, (2009) Local RNA structure alignment with incomplete sequence. Bioinformatics 25: 1236-1243.
15. Mercer TR, Dinger ME, Mattick JS, (2009) Long non-coding RNAs: insights into functions. Nature Reviews Genetics 10: 155-159.
16. Martin JA, Wang Z, (2011) Next-generation transcriptome assembly. Nature Reviews Genetics 12: 671-682.
17. Sun G, Stewart CNJ, Xiao P, Zhang B (2012) MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress. PLoS One 7.
18. Peng X, Gralinski L, Ferris MT, FriemanMB ThomasMJ, et al. (2011) Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. MBio 2.
19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of molecular biology 215: 403-410.
20. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome research 18: 821-829.
21. Schulz MH, Zerbino DR, Vingron M, Birney E, (2012) Oases: robust de novo rna-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092.
22. Warren RL, Sutton GG, Jones SJ, Holt RA, (2007) Assembling millions of short DNA sequences using ssake. Bioinformatics 23: 500-501.
23. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, et al. (2007) RNAmmer2: consistent and rapid annotation of ribosomal rna genes. Nucleic acids research 35: 3100-3108.
24. Vilo C, Dong Q, (2012) Evaluation of the RDP classifier accuracy using 16s rRNA gene variable regions. Metagenomics 1: 1-5.
25. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
26. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proceedings of the National Academy of Sciences 107: 7503-7508.