RegRNA
A Regulatory RNA Motifs and Elements Finder
  Release 1.0, Jan 2006
 
 
 

Related Web Sites and Databases
  • RNAMotif: It searches a database for RNA sequences that match a "motif" describing secondary structure interactions.
  • PatSearch: A pattern matching tool, that can find a well defined pattern against a given sequence(s) or database (primary or specialized) divisions.
  • Transterm: An interactive database providing access to RNA sequences and their associated motifs.
  • UTRScan: The program looks for UTR functional elements by searching through user submitted sequence data for the patterns defined in the UTRsite collection.
  • RibEx: A web server for locating riboswitches and other conserved bacterial regulatory elements.
  • Riboswitch finder: A tool for identification of riboswitch RNAs.

References

Mignone, F., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Kersey, P.J., Duarte, J., Saccone, C. and Pesole, G. (2005) UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res , 33, D141-146.

Grillo, G., Licciulli, F., Liuni, S., Sbisa, E. and Pesole, G. (2003) PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res , 31, 3608-3612.

Jacobs, G.H., Stockwell, P.A., Tate, W.P. and Brown, C.M. (2006) Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res , 34, D37-40.

Bengert, P. and Dandekar, T. (2004) Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res , 32, W154-159.

Abreu-Goodger, C. and Merino, E. (2005) RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res , 33, W690-692.

Cartegni, L., Wang, J., Zhu, Z., Zhang, M.Q. and Krainer, A.R. (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res , 31, 3568-3571.

Macke, T.J., Ecker, D.J., Gutell, R.R., Gautheret, D., Case, D.A. and Sampath, R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res , 29, 4724-4735.

Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res , 34, D108-110.

Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L. and Thanaraj, T.A. (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res , 34, D46-55.

Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res , 34, D140-144.

Hsu, P.W., Huang, H.D., Hsu, S.D., Lin, L.Z., Tsou, A.P., Tseng, C.P., Stadler, P.F., Washietl, S. and Hofacker, I.L. (2006) miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res , 34, D135-139.

Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet , 16, 276-277.

Pertea, M., Lin, X. and Salzberg, S.L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res , 29, 1185-1190.

Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol , 5, R1.

Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res , 31, 3406-3415.

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, D121-124.

Ren, J., Rastegari, B., Condon, A. and Hoos, H.H. (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. Rna , 11, 1494-1504.


Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan
Contact with Dr. Hsien-Da Huang