SRNAdb: A small non-coding RNA database for gram-positive bacteria

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Pischimarov, Jordan ^a   Kuenne, Carsten ^a   Billion, André ^a   Hemberger, Jüergen ^b   Cemič, Franz ^b   Chakraborty, Trinad ^a   Hain, Torsten ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b TECHNISCHE HOCHSCHULE MITTELHESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPARATIVE STUDY; DATA ANALYSIS SOFTWARE; GENE FUNCTION; GENE LOCUS; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEIC ACID DATABASE; PHYLOGENY; PLASMID; REPLICON; RNA SEQUENCE; SEQUENCE ANALYSIS;

DATABASES, GENETIC; GRAM-POSITIVE BACTERIA; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED; SOFTWARE; USER-COMPUTER INTERFACE;

NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 84864823820     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-384     Document Type: Article

References (28)

1. Frohlich KS, Vogel J. Activation of gene expression by small RNA. Curr Opin Microbiol 2009, 12:674-682.
2. Mraheil MA, Billion A, Kuenne C, Pischimarov J, Kreikemeyer B, Engelmann S, Hartke A, Giard JC, Rupnik M, Vorwerk S, Beier M, Retey J, Hartsch T, Jacob A, Cemic F, Hemberger J, Chakraborty T, Hain T. Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application. Microb Biotechnol 2010, 3:658-676.
3. Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009, 136:615-628.
4. Cao Y, Wu J, Liu Q, Zhao Y, Ying X, Cha L, Wang L, Li W. sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA 2010, 16:2051-2057.
5. Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 2007, 35:D145-D148.
6. Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K. The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res 2009, 37:D89-D92.
7. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res 2009, 37:D136-D140.
8. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003, 31:439-441.
9. Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, Yang CD, Ju YW, Huang HD. sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 2009, 37:D150-D154.
10. Pruitt KD, Katz KS, Sicotte H, Maglott DR. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 2000, 16:44-47.
11. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007, 8:R22.
12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
13. Arnvig KB, Young DB. Identification of small RNAs in Mycobacterium tuberculosis. Mol Microbiol 2009, 73:397-408.
14. Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezee-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 2010, 38:6620-6636.
15. Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P, Sogaard-Andersen L, Kallipolitis BH. Identification of small Hfq-binding RNAs in Listeria monocytogenes. RNA 2006, 12:1383-1396.
16. Fouquier DA, Wessner F, Halpern D, Ly-Vu J, Kennedy SP, Serror P, Aurell E, Repoila F. A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis. Nucleic Acids Res 2011, 39:e46.
17. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 2009, 37:7239-7257.
18. Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010, 38:6637-6651.
19. Kumar R, Shah P, Swiatlo E, Burgess SC, Lawrence ML, Nanduri B. Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics 2010, 11:350.
20. Livny J, Teonadi H, Livny M, Waldor MK. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 2008, 3:e3197.
21. Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res 2007, 35:962-974.
22. Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, Pischimarov J, Krawitz C, Retey J, Hartsch T, Chakraborty T, Hain T. The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 2011, 39:4235-4248.
23. Nielsen JS, Olsen AS, Bonde M, Valentin-Hansen P, Kallipolitis BH. Identification of a sigma B-dependent small noncoding RNA in Listeria monocytogenes. J Bacteriol 2008, 190:6264-6270.
24. Perez N, Trevino J, Liu Z, Ho SC, Babitzke P, Sumby P. A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PLoS One 2009, 4:e7668.
25. Rasmussen S, Nielsen HB, Jarmer H. The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 2009, 73:1043-1057.
26. Tezuka T, Hara H, Ohnishi Y, Horinouchi S. Identification and gene disruption of small noncoding RNAs in Streptomyces griseus. J Bacteriol 2009, 191:4896-4904.
27. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M, Johansson J, Cossart P. The Listeria transcriptional landscape from saprophytism to virulence. Nature 2009, 459:950-956.
28. Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 2011, 8:468-477.