RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

RNA

Volumn 17, Issue 11, 2011, Pages 1947-1956

  Cros, Marie Josée ^a   De Monte, Antoine ^b   Mariette, Jérôme ^a   Bardou, Philippe ^a   Grenier Boley, Benjamin ^b   Gautheret, Daniel ^c   Touzet, Hélène ^b   Gaspin, Christine ^a  

^a CEMAGREF   (France)

^b UNIV LILLE   (France)

^c INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

Author keywords

Annotation; Bioinformatics; Noncoding RNA; Prediction

Indexed keywords

UNTRANSLATED RNA;

ARTICLE; BIOINFORMATICS; MOLECULAR GENETICS; ONLINE SYSTEM; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; WEB BROWSER;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; GENOME; INTERNET; NUCLEIC ACID CONFORMATION; RNA, UNTRANSLATED; SOFTWARE;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 80054737356     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2844911     Document Type: Article

References (60)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Amaral PP, Dinger ME, Merce TR, Mattick JS. 2008. The Eukaryotic genome as an RNA machine. Science 319: 1787-1789. (Pubitemid 351451554)
3. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
4. Darty K, Denise A, Ponty Y. 2009. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974-1975.
5. Dsouza M, Larsen N, Overbeek R. 1997. Searching for patterns in genomic data. Trends Genet 13: 497-498. (Pubitemid 28004924)
6. Freyhult E, Gardner PP, Moulton V. 2005. A comparison of RNA folding measures. BMC Bioinformatics 6: 241. doi: 10.1186/1471-2105-6-241.
7. Gardner P, Giegerich R. 2004. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140. doi: 10.1186/1471-2105-5-140.
8. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, et al. 2009. Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136-D140.
9. Gautheret D, Lambert A. 2001. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 313: 1003-1011. (Pubitemid 33081896)
10. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francxois P, Vandenesch F, Gaspin C, et al. 2009. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37: 7239-7257.
11. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158. (Pubitemid 351149713)
12. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Res 36: W70-W74.
13. Hüttenhofer A, Schattner P, Polacek N. 2005. Non-coding RNAs: hope or hype? Trends Genet 21: 289-297. (Pubitemid 40558935)
14. Jacquier A. 2009. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10: 833-844.
15. Jäger D, Sharma CM, Thomsen J, Ehlers C, Vogel J, Schmitz RA. 2009. Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci 106: 21878-21882.
16. Jossinet F, Westhof E. 2005. Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21: 3320-3321. (Pubitemid 41418451)
17. Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K. 2006. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 35: D145-D148. (Pubitemid 46056187)
18. Klein RJ, Eddy SR. 2003. RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 4: 44. doi: 10.1186/1471-2105-4-44.
19. Klein RJ, Misulovin Z, Eddy SR. 2002. Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci 99: 7542-7547. (Pubitemid 34568727)
20. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108. (Pubitemid 47073647)
21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 3497-3500.
22. Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F. 2008. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. Genome Res 18: 888-899. (Pubitemid 351793061)
23. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16. (Pubitemid 38228599)
24. Lestrade L, Weber MJ. 2006. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 1: D158-D162.
25. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, et al. 2002. Apollo: a sequence annotation editor. Genome Biol 3: research0082-0082.14. doi: 10.1186/gb-2002-3-12-research0082.
26. Li L, Xu J, Yang D, Tan X, Wang H. 2010. Computational approaches for microRNA studies: a review. Mamm Genome 21: 1-12.
27. Liu J, Carnilli A. 2010. A broadening world of bacterial small RNAs. Curr Opin Microbiol 13: 18-23.
28. Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R. 2005. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 33: D112-D115. (Pubitemid 40207841)
29. Livny J, Fogel MA, Davis BM, Waldor MK. 2005. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 33: 4096-4105. (Pubitemid 41487270)
30. Livny J, Brencic A, Lory S, Waldor MK. 2006. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34: 3484-3493.
31. Livny J, Teonadi H, Livny M, Waldor MK. 2008. High-throughput, kingdom-wide prediction and annotation of bacterial noncoding RNAs. PLoS ONE 3: e3197. doi: 10.1371/journal.pone.0003197.
32. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. (Pubitemid 27298263)
33. Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R. 2001. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29: 4724-4735. (Pubitemid 33095034)
34. Markham NR, Zuker M. 2008. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453: 3-31.
35. Mendes ND, Freitas AT, Sagot MF. 2009. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 37: 2419-2433.
36. Menzel P, Gorodkin J, Stadler PF. 2009. The tedious task of finding homologous noncoding RNA genes. RNA 15: 2075-2082.
37. Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335-1337.
38. Noé L, Kucherov G. 2005. YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Res 33: W540-W543. (Pubitemid 44529979)
39. Noirot C, Gaspin C, Schiex T, Gouzy J. 2008. LeARN: a platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics 9: 21. doi: 10.1371/journal.pone.0003197.
40. Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
41. Rivas E, Eddy SR. 2001. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2: 8. doi: 10.1186/1471-2105-2-8.
42. Rivas E, Klein RJ, Jones TA, Eddy SR. 2001. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11: 1369-1373. (Pubitemid 32835879)
43. Ruan J, Stormo GD, Zhang W. 2004. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res 32: W146-W149. (Pubitemid 38997317)
44. Schattner P. 2002. Searching for RNA genes using base-composition statistics. Nucleic Acids Res 30: 2076-2082. (Pubitemid 34537606)
45. Schattner P, Barberan-Soler S, Lowe TM. 2006. A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA 12: 15-25. (Pubitemid 43037449)
46. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. 2009. JBrowse: a next-generation genome browser. Genome Res 19: 1630-1638.
47. Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I. 2008. Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology 154: 3175-3187.
48. Steffen P, Voß B, Rehmsmeier M, Reeder J, Giegerich R. 2006. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22: 500-503. (Pubitemid 43231429)
49. Stothard P, Wishart D. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21: 537-539. (Pubitemid 40310241)
50. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, et al. 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956.
51. Touzet H, Perriquet O. 2004. CARNAC: folding families of related RNAs. Nucleic Acids Res 142: W142-W145. (Pubitemid 38997316)
52. Upadhyay R, Bawankar P, Malhotra D, Patankar S. 2005. A screen for conserved sequences with biased base composition identifies noncoding RNAs in the AT-rich genome of Plasmodium falciparum. Mol Biochem Parasitol 144: 149-158. (Pubitemid 41572221)
53. van Bakel H, Nislow C, Blencowe BJ, Hughes TR. 2010. Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371. doi: 10.1371/journal.pbio.1000371.
54. Washietl S, Hofacker IL, Stadler PF. 2005. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci 102: 2454-2459. (Pubitemid 40279397)
55. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136: 615-628.
56. Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, et al. 2002. RNAML: a standard syntax for exchanging RNA information. RNA 8: 707-717. (Pubitemid 34620448)
57. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, et al. 2007. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 35: 4809-4819. (Pubitemid 47250352)
58. Weinberg Z, Perreault J, Meyer MM, Breaker RR. 2009. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature 462: 656-659.
59. Yao Z, Weinberg Z, Ruzzo W. 2006. CMfinder - a covariance model based RNA motif finding algorithm. Bioinformatics 22: 445-452. (Pubitemid 43231419)
60. Zytnicki M, Gaspin C, Schiex T. 2008. DARN! A weighted constraint solver for RNA motif localization. Constraints 13: 91-109.