GISSD: Group I intron sequence and structure database

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Zhou, Yu ^a,b   Lu, Chen ^a   Wu, Qi Jia ^a   Wang, Yu ^a   Sun, Zhi Tao ^a   Deng, Jia Cong ^a   Zhang, Yi ^a  

^a WUHAN UNIVERSITY   (China)

^b UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE TRANSFER RNA;

ALGORITHM; ARTICLE; CHLOROPLAST; COMPUTER PROGRAM; CONSENSUS SEQUENCE; DATA BASE; EXON; GENBANK; GROUP I INTRON SEQUENCE AND STRUCTURE DATABASE; INTERNET; INTRON; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TAXONOMY;

EID: 38549132349     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm766     Document Type: Article

References (20)

1. Burke, J.M., Belfort, M., Cech, T.R., Davies, R.W., Schweyen, R.J., Shub, D.A., Szostak, J.W. and Tabak, H.F. (1987) Structural conventions for group I introns. Nucleic Acids Res., 15, 7217-7221.
2. Cech, T.R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem., 59, 543-568.
3. Vicens, Q. and Cech, T.R. (2006) Atomic level architecture of group I introns revealed. Trends Biochem. Sci., 31, 41-51.
4. Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
5. Li, Z.J. and Zhang, Y. (2005) Predicting the seeondary structures and tertiary interactions of 211 group I introns in IE subgroup. Nucleic Acids Res., 33, 2118-2128.
6. Rangan, P., Masquida, B., Westhof, E. and Woodson, S.A. (2003) Assembly of core helices and rapid tertiary folding of a small bactefial group I ribozyme. Proc. Natl Acad. Sci. USA, 100, 1574-1579.
7. Xiao,M., Leibowitz, M.J. and Zhang, Y. (2003) Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction. Nucleic Acids Res., 31, 3901-3908.
8. Woodson, S.A. (2005) Metal ions and RNA folding: A highly charged topic with a dynamic future. Curr. Opin. Chem. Biol., 9, 104-109.
9. Haugen, P., Simon, D.M. and Bhattacharya, D. (2005) The natural history of group I introns. Trends Genet., 21, 111-119.
10. Borsch, T., Hilu, K.W., Quandt, D., Wilde, V., Neinhuis, C. and Barthlott, W. (2003) Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol., 16, 558-576.
11. Quandt, D. and Stech, M. (2005) Molecular evolution of the trnL (UAA) intron in bryophytes. Mol. Phylogenet. Evol., 36, 429-443.
12. Won, H. and Renner, S.S. (2005) The chloroplast trnT-trnF region in the seed plant lineage Gnetales. J. Mol. Evol., 61, 425-436.
13. Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C. and Willerslev, E. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res., 35, e14.
14. Kuhsel, M.G., Strickland, R. and Palmer, J.D. (1990) An ancient group I intron shared by eubacteria and chloroplasts. Science, 250, 1570-1573.
15. Cannone, J.J., Subramanian, S., Schnara, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Müller, K.M. et al. (2002) The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 15.
16. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R. and Bateman, A. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
17. Nawrocki, E.P. and Eddy, S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
18. Mathews, D.H., Sabina, J., Zuker, M. and Turner. D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
19. Johansen, S. and Haugen, P. (2001) A new nomenclature of group I introns in ribosomal DNA. RNA, 7, 935-936.
20. De Rijk, P., Wuyts, J. and De Wachter, R. (2003) RnaViz2: An improved representation of RNA secondary structure. Bioinformatics, 19 299-300.