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Volumn 8, Issue 2, 2010, Pages 127-134

PsRNA: A computing engine for the comparative identification of putative small RNA locations within intergenic regions

Author keywords

Flanking genes; Intergenic regions; KEGG Orthology; Small RNA

Indexed keywords

RNA; BACTERIAL DNA; BACTERIAL RNA; SMALL NUCLEAR RNA; SPACER DNA;

EID: 77955340353     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(10)60014-9     Document Type: Article
Times cited : (8)

References (25)
  • 1
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNA
    • Storz G. An expanding universe of noncoding RNA. Science 2002, 296:1260-1263.
    • (2002) Science , vol.296 , pp. 1260-1263
    • Storz, G.1
  • 3
    • 0035395606 scopus 로고    scopus 로고
    • Identification of novel small RNAs using comparative genomics and microarrays
    • Wassarman K.M., et al. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 2001, 15:1637-1651.
    • (2001) Genes Dev. , vol.15 , pp. 1637-1651
    • Wassarman, K.M.1
  • 4
    • 34250709662 scopus 로고    scopus 로고
    • Target identification of small noncoding RNAs in bacteria
    • Vogel J., Wagner E.G.H. Target identification of small noncoding RNAs in bacteria. Curr. Opin. Microbiol. 2007, 10:262-270.
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 262-270
    • Vogel, J.1    Wagner, E.G.H.2
  • 5
    • 34247169597 scopus 로고    scopus 로고
    • CsrB sRNA family: sequestration of RNA-binding regulatory proteins
    • Babitzke P., Romeo T. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr. Opin. Microbiol. 2007, 10:156-163.
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 156-163
    • Babitzke, P.1    Romeo, T.2
  • 6
    • 0037133945 scopus 로고    scopus 로고
    • Computational genomics of noncoding RNA genes
    • Eddy S.R. Computational genomics of noncoding RNA genes. Cell 2002, 139:137-140.
    • (2002) Cell , vol.139 , pp. 137-140
    • Eddy, S.R.1
  • 7
    • 0037252684 scopus 로고    scopus 로고
    • Rfam: an RNA family database
    • Griffiths-Jones S., et al. Rfam: an RNA family database. Nucleic Acids Res. 2003, 31:439-441.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 439-441
    • Griffiths-Jones, S.1
  • 8
    • 13444267841 scopus 로고    scopus 로고
    • NONCODE: an integrated knowledge database of non-coding RNAs
    • Liu C., et al. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 2005, 33:D112-D115.
    • (2005) Nucleic Acids Res. , vol.33
    • Liu, C.1
  • 9
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • Kanehisa M., et al. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32:D277-D280.
    • (2004) Nucleic Acids Res. , vol.32
    • Kanehisa, M.1
  • 11
    • 34247194278 scopus 로고    scopus 로고
    • Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention
    • Sridhar J., Rafi Z.A. 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
  • 12
    • 41849147481 scopus 로고    scopus 로고
    • Identification of novel genomic islands associated with small RNAs
    • Sridhar J., Rafi Z.A. Identification of novel genomic islands associated with small RNAs. In Silico Biol. 2007, 7:601-611.
    • (2007) In Silico Biol. , vol.7 , pp. 601-611
    • Sridhar, J.1    Rafi, Z.A.2
  • 13
    • 77955324319 scopus 로고    scopus 로고
    • Functional annotations in bacterial genomes based on small RNA signatures
    • Sridhar J., Rafi Z.A. Functional annotations in bacterial genomes based on small RNA signatures. Bioinformation 2008, 2:284-295.
    • (2008) Bioinformation , vol.2 , pp. 284-295
    • Sridhar, J.1    Rafi, Z.A.2
  • 14
    • 15044341082 scopus 로고    scopus 로고
    • Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    • Tiffin N., et al. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res. 2005, 33:1544-1552.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1544-1552
    • Tiffin, N.1
  • 15
    • 27544472676 scopus 로고    scopus 로고
    • Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
    • Mao X., et al. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005, 21:3787-3793.
    • (2005) Bioinformatics , vol.21 , pp. 3787-3793
    • Mao, X.1
  • 16
    • 1542327668 scopus 로고    scopus 로고
    • Trends between gene content and genome size in prokaryotic species with larger genomes
    • Konstantinidis K.T., Tiedje J.M. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. USA 2004, 101:3160-3165.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 3160-3165
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 17
    • 77955320670 scopus 로고    scopus 로고
    • Identification of ortholog groups in KEGG/SSDB by considering domain structures
    • Itoh M., et al. Identification of ortholog groups in KEGG/SSDB by considering domain structures. Genome Informatics 2002, 13:342-343.
    • (2002) Genome Informatics , vol.13 , pp. 342-343
    • Itoh, M.1
  • 18
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • Rivas E., Eddy S.R. 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
  • 19
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • Washietl S., et al. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 2005, 102:2454-2459.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2454-2459
    • Washietl, S.1
  • 20
    • 13444252847 scopus 로고    scopus 로고
    • Rfam: annotating non-coding RNAs in complete genomes
    • Griffiths-Jones S., et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 2005, 33:D121-D124.
    • (2005) Nucleic Acids Res. , vol.33
    • Griffiths-Jones, S.1
  • 21
    • 0037387973 scopus 로고    scopus 로고
    • A survey of small RNA-encoding genes in Escherichia coli
    • Hershberg R., et al. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 2003, 31:1813-1820.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1813-1820
    • Hershberg, R.1
  • 22
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1462.
    • (1997) Science , vol.277 , pp. 1453-1462
    • Blattner, F.R.1
  • 23
    • 0020445415 scopus 로고
    • Identification of two genes immediately downstream from the polA gene of Escherichia coli
    • Joyce C.M., Grindley N.D. Identification of two genes immediately downstream from the polA gene of Escherichia coli. J. Bacteriol. 1982, 152:1211-1219.
    • (1982) J. Bacteriol. , vol.152 , pp. 1211-1219
    • Joyce, C.M.1    Grindley, N.D.2
  • 24
    • 33748082663 scopus 로고    scopus 로고
    • How to become a uropathogen: comparative genomic anlaysis of extraintestinal pathogenic Escherichia coli strains
    • Brzuszkiewicz E., et al. How to become a uropathogen: comparative genomic anlaysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl. Acad. Sci. USA 2006, 103:12879-12884.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 12879-12884
    • Brzuszkiewicz, E.1
  • 25
    • 67651183730 scopus 로고    scopus 로고
    • Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention II
    • Sridhar J., et al. Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention II. OMICS 2009, 13:261-284.
    • (2009) OMICS , vol.13 , pp. 261-284
    • Sridhar, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.