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Volumn 7, Issue , 2013, Pages 83-95

Computational small RNA prediction in bacteria

Author keywords

Base composition; Comparative genomics; ncRNA; sRNA prediction; Structure stability; Transcriptional signal

Indexed keywords

SMALL UNTRANSLATED RNA;

EID: 84874902310     PISSN: 11779322     EISSN: None     Source Type: Journal    
DOI: 10.4137/BBI.S11213     Document Type: Review
Times cited : (33)

References (60)
  • 2
    • 0038341634 scopus 로고    scopus 로고
    • RNA-mediated control of virulence gene expression in bacterial pathogens
    • Johansson J, Cossart P. RNA-mediated control of virulence gene expression in bacterial pathogens. Trends Microbiol. 2003;11:280-5.
    • (2003) Trends Microbiol , vol.11 , pp. 280-285
    • Johansson, J.1    Cossart, P.2
  • 4
    • 77958028354 scopus 로고    scopus 로고
    • Regulatory RNA in Bacterial Pathogens
    • Papenfort K, Vogel J. Regulatory RNA in Bacterial Pathogens. Cell Host and Microbe. 2010;8:116-27.
    • (2010) Cell Host and Microbe , vol.8 , pp. 116-127
    • Papenfort, K.1    Vogel, J.2
  • 5
    • 84874833635 scopus 로고    scopus 로고
    • Regulation of virulence in Francisella tularensis by small noncoding RNAs
    • doi:10.1038/npre.2011.5965.1
    • Postic G, Frapy E, Dupuis M, et al. Regulation of virulence in Francisella tularensis by small noncoding RNAs. Nature Preceedings. 2011. doi:10.1038/npre.2011.5965.1.
    • (2011) Nature Preceedings
    • Postic, G.1    Frapy, E.2    Dupuis, M.3
  • 7
    • 34447254589 scopus 로고    scopus 로고
    • RyhB, an Iron-Responsive Small RNA Molecule, Regulates Shigella dysenteriae Virulence
    • Murphy ER, Payne SM. RyhB, an Iron-Responsive Small RNA Molecule, Regulates Shigella dysenteriae Virulence. Infect Immun. 2007;75:3470-7.
    • (2007) Infect Immun , vol.75 , pp. 3470-3477
    • Murphy, E.R.1    Payne, S.M.2
  • 8
    • 41849139346 scopus 로고    scopus 로고
    • Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
    • Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, et al. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res. 2008;36:1913-27.
    • (2008) Nucleic Acids Res , vol.36 , pp. 1913-1927
    • Padalon-Brauch, G.1    Hershberg, R.2    Elgrably-Weiss, M.3
  • 9
    • 33748674467 scopus 로고    scopus 로고
    • Small RNAs in Bacterial Cell to Cell Communication
    • Kay E, Reimmann C, Haas D. Small RNAs in Bacterial Cell to Cell Communication. Microbe. 2006;1:63-9.
    • (2006) Microbe , vol.1 , pp. 63-69
    • Kay, E.1    Reimmann, C.2    Haas, D.3
  • 10
    • 72049118448 scopus 로고    scopus 로고
    • Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaerioides
    • Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G. Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaerioides. Mol Microbiol. 2009;74:1497-512.
    • (2009) Mol Microbiol , vol.74 , pp. 1497-1512
    • Berghoff, B.A.1    Glaeser, J.2    Sharma, C.M.3    Vogel, J.4    Klug, G.5
  • 11
    • 58149139033 scopus 로고    scopus 로고
    • A rough guide to the noncoding RNA world of Salmonella
    • Vogel J. A rough guide to the noncoding RNA world of Salmonella. Mol Microbiol. 2009;71:1-11.
    • (2009) Mol Microbiol , vol.71 , pp. 1-11
    • Vogel, J.1
  • 12
    • 0035954304 scopus 로고    scopus 로고
    • Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    • Argaman L, Hershberg R, Vogel J, et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol. 2001;11:941-50.
    • (2001) Curr Biol , vol.11 , pp. 941-950
    • Argaman, L.1    Hershberg, R.2    Vogel, J.3
  • 13
    • 0035395606 scopus 로고    scopus 로고
    • Identification of novel small RNAs using comparative genomics and microarrays
    • Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 2001;15:1637-51.
    • (2001) Genes Dev , vol.15 , pp. 1637-1651
    • Wassarman, K.M.1    Repoila, F.2    Rosenow, C.3    Storz, G.4    Gottesman, S.5
  • 14
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2001;2:8.
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 15
    • 0036271043 scopus 로고    scopus 로고
    • A Bioinformatics based approach to discover small RNA genes in the Escherichia coli genome
    • Chen S, Lesnik EA, Hall TA, et al. A Bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems. 2002;65:157-77.
    • (2002) Biosystems , vol.65 , pp. 157-177
    • Chen, S.1    Lesnik, E.A.2    Hall, T.A.3
  • 17
    • 0141850376 scopus 로고    scopus 로고
    • Intergenic sequence inspector: Searching and identifying bacterial RNAs
    • Pichon C, Felden B. Intergenic sequence inspector: searching and identifying bacterial RNAs. Nucleic Acids Res. 2003;19:1707-9.
    • (2003) Nucleic Acids Res , vol.19 , pp. 1707-1709
    • Pichon, C.1    Felden, B.2
  • 18
    • 22844436749 scopus 로고    scopus 로고
    • sRNAPredict: An integrative computational approach to identify sRNAs in bacterial genomes
    • Livny J, Fogel MA, Davis BM, Waldor MK. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res. 2005;33:4096-105.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4096-4105
    • Livny, J.1    Fogel, M.A.2    Davis, B.M.3    Waldor, M.K.4
  • 19
    • 77957788941 scopus 로고    scopus 로고
    • sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes
    • Sridhar J, Narmada SR, Sabarinathan R, et al. sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes. PLoS ONE. 2010;5:e11970.
    • (2010) PLoS ONE , vol.5
    • Sridhar, J.1    Narmada, S.R.2    Sabarinathan, R.3
  • 20
    • 79251567076 scopus 로고    scopus 로고
    • nocoRNAc: Characterization of noncoding RNAs in prokaryotes
    • Herbig A, Nieselt K. nocoRNAc: Characterization of noncoding RNAs in prokaryotes. BMC Bioinformatics. 2011;12:40.
    • (2011) BMC Bioinformatics , vol.12 , pp. 40
    • Herbig, A.1    Nieselt, K.2
  • 21
    • 58149191274 scopus 로고    scopus 로고
    • Rfam: Updates to the RNA families database
    • Gardner PP, Daub J, Tate JG, et al. Rfam: updates to the RNA families database. Nucl Acids Res. 2009;37:D136-40.
    • (2009) Nucl Acids Res , vol.37
    • Gardner, P.P.1    Daub, J.2    Tate, J.G.3
  • 24
    • 0029986908 scopus 로고    scopus 로고
    • Palingol: A declarative programming language to describe nucleic acids' secondary structures and to scan sequence databases
    • Billoud B, Kontic M, Viari A. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence databases. Nucleic Acids Res. 1996;24:1395-403.
    • (1996) Nucleic Acids Res , vol.24 , pp. 1395-1403
    • Billoud, B.1    Kontic, M.2    Viari, A.3
  • 26
    • 0025095711 scopus 로고
    • Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA
    • Gautheret D, Major F, Cedergren F. Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. CABIOS. 1990:325-11.
    • (1990) CABIOS , pp. 325-411
    • Gautheret, D.1    Major, F.2    Cedergren, F.3
  • 27
    • 84874922878 scopus 로고    scopus 로고
    • RNALfoldz: Efficient prediction of thermodynamically stable, local secondary structures, Lecture notes in informatics
    • Braunschweig, Germany
    • Gruber AR, Bernhart SH, Zhou Y, Hofacker IL. RNALfoldz: efficient prediction of thermodynamically stable, local secondary structures, Lecture notes in informatics. Proceedings of German Conference on Bioinformatics 2010. Braunschweig, Germany.
    • (2010) Proceedings of German Conference On Bioinformatics
    • Gruber, A.R.1    Bernhart, S.H.2    Zhou, Y.3    Hofacker, I.L.4
  • 28
    • 79960694944 scopus 로고    scopus 로고
    • sTarPicker: A Method for Efficient Prediction of Bacterial sRNA Targets Based on a Two-Step Model for Hybridization
    • Ying X, Cao Y, Wu J, Liu Q, Cha L, Li W. sTarPicker: A Method for Efficient Prediction of Bacterial sRNA Targets Based on a Two-Step Model for Hybridization. PLoS ONE. 2011;6:e22705.
    • (2011) PLoS ONE , vol.6
    • Ying, X.1    Cao, Y.2    Wu, J.3    Liu, Q.4    Cha, L.5    Li, W.6
  • 29
    • 36448976216 scopus 로고    scopus 로고
    • Prediction of small, noncoding RNAs in bacteria using heterogenous data
    • Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogenous data. J Math Biol. 2008;56:183-200.
    • (2008) J Math Biol , vol.56 , pp. 183-200
    • Tjaden, B.1
  • 31
    • 32644439243 scopus 로고    scopus 로고
    • Experimental approaches to identify noncoding RNAs
    • Huttenhofer A, Vogel J. Experimental approaches to identify noncoding RNAs. Nucl Acids Res. 2006;34:635-46.
    • (2006) Nucl Acids Res , vol.34 , pp. 635-646
    • Huttenhofer, A.1    Vogel, J.2
  • 32
    • 34250709662 scopus 로고    scopus 로고
    • Target identification of small noncoding RNAs in bacteria
    • Vogel J, Wagner EGH. Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol. 2007;10:262-70.
    • (2007) Curr Opin Microbiol , vol.10 , pp. 262-270
    • Vogel, J.1    Wagner, E.G.H.2
  • 33
  • 34
    • 63749124071 scopus 로고    scopus 로고
    • Biocomputational prediction of noncoding RNAs in model cyanobacteria
    • Voß B, Georg J, Schön V, Ude S, Hess WR. Biocomputational prediction of noncoding RNAs in model cyanobacteria. BMC Genomics. 2009;10:123.
    • (2009) BMC Genomics , vol.10 , pp. 123
    • Voß, B.1    Georg, J.2    Schön, V.3    Ude, S.4    Hess, W.R.5
  • 35
    • 77950914774 scopus 로고    scopus 로고
    • A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
    • Schluter JP, Reinkensmeier J, Daschkey S, et al. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 2010;11:245.
    • (2010) BMC Genomics , vol.11 , pp. 245
    • Schluter, J.P.1    Reinkensmeier, J.2    Daschkey, S.3
  • 36
    • 78149264799 scopus 로고    scopus 로고
    • Identification of small RNAs in Francisella tularensis
    • Postic G, Frapy E, Dupuis M, et al. Identification of small RNAs in Francisella tularensis. BMC Genomics. 2010;11:625.
    • (2010) BMC Genomics , vol.11 , pp. 625
    • Postic, G.1    Frapy, E.2    Dupuis, M.3
  • 37
    • 79251575899 scopus 로고    scopus 로고
    • Identification and functional characterization of small noncoding RNAs in Xanthomonas oryzae pathovar oryzae
    • Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT. Identification and functional characterization of small noncoding RNAs in Xanthomonas oryzae pathovar oryzae. BMC Genomics. 2011;12:87.
    • (2011) BMC Genomics , vol.12 , pp. 87
    • Liang, H.1    Zhao, Y.T.2    Zhang, J.Q.3    Wang, X.J.4    Fang, R.X.5    Jia, Y.T.6
  • 39
    • 0035834489 scopus 로고    scopus 로고
    • Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles
    • Gautheret D, Lambert AA. Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Bio. 2001;313:1003-11.
    • (2001) J Mol Bio , vol.313 , pp. 1003-1011
    • Gautheret, D.1    Lambert, A.A.2
  • 41
    • 0027968068 scopus 로고
    • CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-80.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 42
    • 4344584927 scopus 로고    scopus 로고
    • MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
    • Coventry A, Kleitman DJ, Berger B. MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A. 2004;101:12102-7.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 12102-12107
    • Coventry, A.1    Kleitman, D.J.2    Berger, B.3
  • 45
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999;288:911-40.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 47
    • 3242882720 scopus 로고    scopus 로고
    • CARNAC: Folding families of related RNAs
    • Touzet H, Perriquet O. CARNAC: folding families of related RNAs. Nucleic Acids Res. 2004;32:W142-5.
    • (2004) Nucleic Acids Res , vol.32
    • Touzet, H.1    Perriquet, O.2
  • 48
    • 34447499141 scopus 로고    scopus 로고
    • Rapid, accurate, computational discovery of Rho-independent transcriptional terminators illuminates their relationship to DNA uptake
    • Kingsford C, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcriptional terminators illuminates their relationship to DNA uptake. Genome Biol. 2007;8:R22.
    • (2007) Genome Biol , vol.8
    • Kingsford, C.1    Ayanbule, K.2    Salzberg, S.L.3
  • 50
    • 52449093583 scopus 로고    scopus 로고
    • High-Throughput, kingdom wide prediction and annotation of bacterial noncoding RNAs
    • Livny J, Teonadi H, Livny M, Waldor MK. High-Throughput, kingdom wide prediction and annotation of bacterial noncoding RNAs. PLoS One. 2008;3:e3197.
    • (2008) PLoS One , vol.3
    • Livny, J.1    Teonadi, H.2    Livny, M.3    Waldor, M.K.4
  • 51
    • 0035477134 scopus 로고    scopus 로고
    • A Computational approach to identify genes for functional RNAs in genomic sequences
    • Carter RJ, Dubchak I, Holbrook SR. A Computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res. 2001;29:3928-38.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3928-3938
    • Carter, R.J.1    Dubchak, I.2    Holbrook, S.R.3
  • 52
    • 0037188546 scopus 로고    scopus 로고
    • Noncoding RNA genes identified in AT-rich hyperthermophiles
    • Klein RJ, Misulovin Z, Eddy SR. Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci U S A. 2002;99:7542-7.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 7542-7547
    • Klein, R.J.1    Misulovin, Z.2    Eddy, S.R.3
  • 53
    • 34247194278 scopus 로고    scopus 로고
    • Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention
    • Sridhar J, Rafi ZA. Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention. OMICS. 2007;11:74-99.
    • (2007) OMICS , vol.11 , pp. 74-99
    • Sridhar, J.1    Rafi, Z.A.2
  • 54
    • 84862188104 scopus 로고    scopus 로고
    • NAPP: The nucleic acid phylogenetic profile database
    • doi:10.1093/nar/gkr807
    • Ott A, Idali A, Marchais A, Gautheret D. NAPP: the nucleic acid phylogenetic profile database. Nucl Acids Res. 2011. doi:10.1093/nar/gkr807.
    • (2011) Nucl Acids Res
    • Ott, A.1    Idali, A.2    Marchais, A.3    Gautheret, D.4
  • 55
    • 77955340353 scopus 로고    scopus 로고
    • PsRNA: A Computing Engine for the comparative identification of putative small RNA locations within intergenic regions
    • Sridhar J, Sowmya G, Sekar K, Rafi ZA. PsRNA: A Computing Engine for the comparative identification of putative small RNA locations within intergenic regions. Genomics Proteomics Bioinformatics. 2010;8:127-34.
    • (2010) Genomics Proteomics Bioinformatics , vol.8 , pp. 127-134
    • Sridhar, J.1    Sowmya, G.2    Sekar, K.3    Rafi, Z.A.4
  • 56
    • 57249116905 scopus 로고    scopus 로고
    • Small RNA gene identification and mRNA target predictions in bacteria
    • Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics. 2008;24:2807-13.
    • (2008) Bioinformatics , vol.24 , pp. 2807-2813
    • Pichon, C.1    Felden, B.2
  • 57
    • 84860392511 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of small RNA genes in bacteria
    • Lu X, Goodrich-Blair H, Tjaden B. Assessing computational tools for the discovery of small RNA genes in bacteria. RNA. 2011;17:1635-47.
    • (2011) RNA , vol.17 , pp. 1635-1647
    • Lu, X.1    Goodrich-Blair, H.2    Tjaden, B.3
  • 58
    • 77949425194 scopus 로고    scopus 로고
    • The primary transcriptome of the major human pathogen. Helicobacter pylori
    • Sharma CM, Hoffman S, Darfeuille F, et al. The primary transcriptome of the major human pathogen. Helicobacter pylori. Nature. 2010;464:250-5.
    • (2010) Nature , vol.464 , pp. 250-255
    • Sharma, C.M.1    Hoffman, S.2    Darfeuille, F.3
  • 59
    • 84856065621 scopus 로고    scopus 로고
    • RNA-Seq based transcriptional map of bovine respiratory disease pathogen "Histophilu somni 2336"
    • Kumar R, Lawrence ML, Watt J, Cooksey AM, Burgess SC, Nanduri B. RNA-Seq based transcriptional map of bovine respiratory disease pathogen "Histophilu somni 2336". PLoS One. 2012;7(1):e0029435.
    • (2012) PLoS One , vol.7 , Issue.1
    • Kumar, R.1    Lawrence, M.L.2    Watt, J.3    Cooksey, A.M.4    Burgess, S.C.5    Nanduri, B.6
  • 60
    • 84859037548 scopus 로고    scopus 로고
    • A genomewide indentification anlaysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-seq and conservation analysis
    • Pellin D, Miotto P, Ambrosi A, Cirillo DM, Serio CD. A genomewide indentification anlaysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-seq and conservation analysis. PLoS One. 2012;7(3):e0032733.
    • (2012) PLoS One , vol.7 , Issue.3
    • Pellin, D.1    Miotto, P.2    Ambrosi, A.3    Cirillo, D.M.4    Serio, C.D.5


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