NAPP: The nucleic acid phylogenetic profile database

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Ott, Alban ^a   Idali, Anouar ^a   Marchais, Antonin ^b   Gautheret, Daniel ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE CLUSTER; GENETIC ANALYSIS; GENETIC CONSERVATION; INTERNET; NUCLEIC ACID DATABASE; NUCLEIC ACID PHYLOGENETIC PROFILE DATABASE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA GENE; RNA STRUCTURE; SEQUENCE ANALYSIS; WEB BROWSER;

BACILLUS SUBTILIS; BASE SEQUENCE; CONSERVED SEQUENCE; DATABASES, NUCLEIC ACID; GENOME, ARCHAEAL; GENOME, BACTERIAL; PHYLOGENY; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED;

EID: 84862188104     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr807     Document Type: Article

References (12)

1. Backofen,R. and Hess,W.R. (2010) Computational prediction of sRNAs and their targets in bacteria. RNA Biol., 7, 33-42.
2. Rivas,E. and Eddy,S.R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2, 8.
3. Washietl,S., Hofacker,I.L. and Stadler,P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454-2459. (Pubitemid 40279397)
4. Livny,J., Teonadi,H., Livny,M. and Waldor,M.K. (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE, 3, e3197.
5. Papenfort,K., Bouvier,M., Mika,F., Sharma,C.M. and Vogel,J. (2010) Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. Proc. Natl Acad. Sci. USA., 107, 20435-20440.
6. Marchais,A., Naville,M., Bohn,C., Bouloc,P. and Gautheret,D. (2009) Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res., 19, 1084-1092.
7. Marchais,A., Duperrier,S., Durand,S., Gautheret,D. and Stragier,P. (2011) CsfG, a family of sporulation-specific, small non-coding RNA highly conserved in endospore formers. RNA Biol., 8, 358-364.
8. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
9. Gardner,P.P., Daub,J., Tate,J.G., Nawrocki,E.P., Kolbe,D.L., Lindgreen,S., Wilkinson,A.C., Finn,R.D., Griffiths-Jones,S., Eddy,S.R. et al. (2008) Rfam: Updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
10. Lu,X., Goodrich-Blair,H. and Tjaden,B. (2011) Assessing computational tools for the discovery of small RNA genes in bacteria. RNA, 17, 1635-1647.
11. de Hoon,M.J., Makita,Y., Nakai,K. and Miyano,S. (2005) Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol., 1, e25.
12. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288. (Pubitemid 29190328)