An RNA mapping data base for curating RNA structure mapping experiments

Bioinformatics

Volumn 28, Issue 22, 2012, Pages 3006-3008

  Cordero, Pablo ^a   Lucks, Julius B ^b   Das, Rhiju ^a  

^a STANFORD UNIVERSITY   (United States)

^b School of Chemical and Molecular Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER; COMPUTER PROGRAM; CONFORMATION; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; COMPUTERS; DATABASES, NUCLEIC ACID; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE;

EID: 84869472916     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts554     Document Type: Article

References (34)

1. Adilakshmi, T. et al. (2006) Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res., 34, e6.
2. Aviran, S. et al. (2011) Modeling and automation of sequencing-based characterization of RNA structure. Proc. Natl Acad. Sci., 108, 11069-11074.
3. Bateman, A. et al. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.
4. Bernstein, F.C. et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542. (Pubitemid 8109216)
5. Culver, G. et al. (1999) Identification of an RNA-protein bridge spanning the ribosomal subunit interface. Science, 285, 2133-2135. (Pubitemid 29451432)
6. Darty, K. et al. (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
7. Das, R. et al. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods, 7, 291-294.
8. Deigan, K.E. et al. (2009) Accurate SHAPE directed RNA structure determination. Proc. Natl Acad. Sci., 106, 97-100.
9. Eickbush, T.H. and Eickbush, D. (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics, 175, 477-485. (Pubitemid 46798252)
10. Getz, M. et al. (2007) Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers, 86, 384-402. (Pubitemid 47237806)
11. Kertesz, M. et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature, 267, 103-107.
12. Kladwang, W. et al. (2011) A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA, 17, 522-534.
13. Kladwang, W. and Das, R. (2010) A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix. Biochemistry, 49, 7414-7416.
14. Kladwang, W. et al. (2011) Two-dimensional chemical mapping of non-coding RNAs. Nat. Chem., 3, 954-962.
15. Kladwang, W. et al. (2011) Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry, 50, 8049-8056.
16. Kudla, G. et al. (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science, 324, 255-258.
17. Low, J.T. and Weeks, K.M. (2010) SHAPE-directed RNA secondary structure prediction. Methods, 52, 150-158.
18. Lucks, J.B. et al. (2011) Multiplexed RNA structure characterization with selective 20-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc. Natl. Acad. Sci., 108, 11063-11068.
19. Mathews, D. and Turner, D. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278. (Pubitemid 43831654)
20. Mitra, S. et al. (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res, 36, e63.
21. Mortimer, S.A. and Weeks, K.M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE Chemistry. J. Am. Chem. Soc., 129, 4144-4145. (Pubitemid 46595421)
22. Nudler, E. and Mironov, A.S. (2004) The riboswitch control of bacterial metabolism. Trends Biochem. Sci., 29, 11-17. (Pubitemid 38068475)
23. Rocca-Serra, P. et al. (2011) Sharing and archiving nucleic acid structure mapping data. RNA, 17, 1204-1212.
24. Spahn, C.M.T. et al. (2001) Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit. Science, 291, 1959-1962. (Pubitemid 32216995)
25. Underwood, J.G. et al. (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods, 7, 995-1001.
26. Ulrich, E.L. et al. (2007) BioMagResBank. Nucleic Acids Res., 36, D402-D408. (Pubitemid 351149757)
27. Varani, G. and Tinoco, I. (1991) RNA structure andNMR spectroscopy. Quart. Rev. Biophys., 24, 479-532.
28. Vasa, S.M. et al. (2008) ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA, 14, 1979-1990.
29. Waldsich, C. (2008) Dissecting RNA folding by nucleotide analog interference mapping (NAIM). Nat. Protoc., 3, 811-823. (Pubitemid 351639025)
30. Watts, J.M. et al. (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature, 460, 711-716.
31. Wilkinson, K.A. et al. (2006) Selective 29-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc., 1, 1610-1616.
32. Yanofsky, C. (2004) The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. Trends Genet., 20, 367-374. (Pubitemid 38943027)
33. Yoon, S. et al. (2011) HiTRACE: high-throughput robust analysis for capillary electrophoresis. Bioinformatics, 27, 1798-805.
34. Zheng, Q. et al. (2010) Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet., 6, e1001141.