메뉴 건너뛰기




Volumn 39, Issue 8, 2011, Pages 3418-3426

The suboptimal structures find the optimal RNAs: Homology search for bacterial non-coding RNAs using suboptimal RNA structures

Author keywords

[No Author keywords available]

Indexed keywords

RNA 6S; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

EID: 79955637005     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1186     Document Type: Article
Times cited : (29)

References (21)
  • 1
    • 0034625237 scopus 로고    scopus 로고
    • 6S RNA regulates E. coli RNA polymerase activity
    • Wassarman, K.M. and Storz, G. (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell, 101, 613-623.
    • (2000) Cell , vol.101 , pp. 613-623
    • Wassarman, K.M.1    Storz, G.2
  • 2
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • DOI 10.1016/j.sbi.2005.05.003, PII S0959440X05000874
    • Tucker, B.J. and Breaker, R.R. (2005) Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol., 15, 342-348. (Pubitemid 40826454)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS. , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 3
    • 29044443534 scopus 로고    scopus 로고
    • How to find small non-coding RNAs in bacteria
    • DOI 10.1515/BC.2005.140
    • Vogel, J. and Sharma, C.M. (2005) How to find small non-coding RNAs in bacteria. Biol. Chem., 386, 1219-1238. (Pubitemid 41790806)
    • (2005) Biological Chemistry , vol.386 , Issue.12 , pp. 1219-1238
    • Vogel, J.1    Sharma, C.M.2
  • 4
    • 0035865320 scopus 로고    scopus 로고
    • Guide to the draft human genome
    • DOI 10.1038/35057000
    • Wolfsberg, T.G., McEntyre, J. and Schuler, G.D. (2001) Guide to the draft human genome. Nature, 409, 824-826. (Pubitemid 32165332)
    • (2001) Nature , vol.409 , Issue.6822 , pp. 824-826
    • Wolfsberg, T.G.1    McEntyre, J.2    Schuler, G.D.3
  • 5
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • Gardner, P.P. and Giegerich, R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140.
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 7
    • 0037154430 scopus 로고    scopus 로고
    • Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of Bacillus subtilis genome
    • DOI 10.1016/S0378-1097(01)00551-1, PII S0378109701005511
    • Ando, Y., Asari, S., Suzuma, S., Yamane, K. and Nakamura, K. (2002) Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of Bacillus subtilis genome. FEMS Microbiol. Lett., 207, 29-33. (Pubitemid 34214801)
    • (2002) FEMS Microbiology Letters , vol.207 , Issue.1 , pp. 29-33
    • Ando, Y.1    Asari, S.2    Suzuma, S.3    Yamane, K.4    Nakamura, K.5
  • 8
    • 0036667443 scopus 로고    scopus 로고
    • Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome
    • Suzuma, S., Asari, S., Bunai, K., Yoshino, K., Ando, Y., Kakeshita, H., Fujita, M., Nakamura, K. and Yamane, K. (2002) Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome. Microbiology, 148, 2591-2598.
    • (2002) Microbiology , vol.148 , pp. 2591-2598
    • Suzuma, S.1    Asari, S.2    Bunai, K.3    Yoshino, K.4    Ando, Y.5    Kakeshita, H.6    Fujita, M.7    Nakamura, K.8    Yamane, K.9
  • 9
    • 18344371528 scopus 로고    scopus 로고
    • A highly conserved 6S RNA structure is required for regulation of transcription
    • DOI 10.1038/nsmb917
    • Trotochaud, A.E. and Wassarman, K.M. (2005) A highly conserved 6S RNA structure is required for regulation of transcription. Nat. Struct. Mol. Biol., 12, 313-319. (Pubitemid 43093085)
    • (2005) Nature Structural and Molecular Biology , vol.12 , Issue.4 , pp. 313-319
    • Trotochaud, A.E.1    Wassarman, K.M.2
  • 10
    • 17844379221 scopus 로고    scopus 로고
    • 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter
    • DOI 10.1261/rna.7286705
    • Barrick, J.E., Sudarsan, N., Weinberg, Z., Ruzzo, W.L. and Breaker, R.R. (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA, 11, 774-784. (Pubitemid 40594342)
    • (2005) RNA , vol.11 , Issue.5 , pp. 774-784
    • Barrick, J.E.1    Sudarsan, N.2    Weinberg, Z.3    Ruzzo, W.L.4    Breaker, R.R.5
  • 11
    • 34447499141 scopus 로고    scopus 로고
    • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    • Kingsford, C.L., Ayanbule, K. and Salzberg, S.L. (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol., 8, R22.
    • (2007) Genome Biol. , vol.8
    • Kingsford, C.L.1    Ayanbule, K.2    Salzberg, S.L.3
  • 12
  • 14
    • 45149084297 scopus 로고    scopus 로고
    • The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis
    • DOI 10.1111/j.1365-2958.2008.06256.x
    • Krasny, L., Tiserova, H., Jonak, J., Rejman, D. and Sanderova, H. (2008) The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol. Microbiol., 69, 42-54. (Pubitemid 351832752)
    • (2008) Molecular Microbiology , vol.69 , Issue.1 , pp. 42-54
    • Krasny, L.1    Tiserova, H.2    Jonak, J.3    Rejman, D.4    Sanderova, H.5
  • 16
    • 23144440350 scopus 로고    scopus 로고
    • DINAMelt web server for nucleic acid melting prediction
    • DOI 10.1093/nar/gki591
    • Markham, N.R. and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581. (Pubitemid 44529988)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Markham, N.R.1    Zuker, M.2
  • 18
    • 70849110294 scopus 로고    scopus 로고
    • RNA secondary structure analysis using the Vienna RNA package
    • Chapter 12, Unit 12 12
    • Hofacker, I.L. (2004) RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics, Chapter 12, Unit 12 12.
    • (2004) Curr. Protoc. Bioinformatics
    • Hofacker, I.L.1
  • 19
    • 44849094549 scopus 로고    scopus 로고
    • Biocomputational prediction of small non-coding RNAs in Streptomyces
    • Panek, J., Bobek, J., Mikulik, K., Basler, M. and Vohradsky, J. (2008) Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics, 9, 217.
    • (2008) BMC Genomics , vol.9 , pp. 217
    • Panek, J.1    Bobek, J.2    Mikulik, K.3    Basler, M.4    Vohradsky, J.5
  • 21
    • 70449361863 scopus 로고    scopus 로고
    • De novo computational prediction of non-coding RNA genes in prokaryotic genomes
    • Tran, T.T., Zhou, F., Marshburn, S., Stead, M., Kushner, S.R. and Xu, Y. (2009) De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics, 25, 2897-2905.
    • (2009) Bioinformatics , vol.25 , pp. 2897-2905
    • Tran, T.T.1    Zhou, F.2    Marshburn, S.3    Stead, M.4    Kushner, S.R.5    Xu, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.