MicroInspector: A web tool for detection of miRNA binding sites in an RNA sequence

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Rusinov, Ventsislav ^a,b   Baev, Vesselin ^a,b   Minkov, Ivan Nikiforov ^b   Tabler, Martin ^a  

^a INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

^b UNIVERSITY OF PLOVDIV   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ACCESS TO INFORMATION; ARABIDOPSIS; ARTICLE; BINDING SITE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DROSOPHILA MELANOGASTER; ENERGY; EXPERIMENTATION; INTERNET; NONHUMAN; PRIORITY JOURNAL; PROTEIN TARGETING; REGISTER; RNA ANALYSIS; RNA SEQUENCE; SKILL; TEMPERATURE; CLIENT SERVER APPLICATION; COMPUTER INTERFACE; GENETIC DATABASE; HUMAN; RNA BINDING; BASE PAIRING; CHEMISTRY; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS;

ARABIDOPSIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER;

BASE PAIRING; BINDING SITES; INTERNET; MICRORNAS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 23144449159     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki364     Document Type: Article

References (29)

1. Lagos-Quintana,M., Rauhut,R., Lendeckel,W. and Tuschl,T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
2. Lau,N.C., Lim,L.P., Weinstein,E.G. and Bartel,D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
3. Lee,R.C. and Ambros,V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
4. Ambros,V. (2001) microRNAs: Tiny regulators with great potential. Cell, 107, 823-826.
5. Ambros,V. (2003) MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing. Cell, 113, 673-676.
6. Ambros,V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
7. He,L. and Hannon,G.J. (2004) MicroRNAs: Small RNAs with a big role in gene regulation. Nature Rev. Genet., 5, 522-531.
8. Nelson,P., Kiriakidou,M., Sharma,A., Maniataki,E. and Mourelatos,Z. (2003) The microRNA world: Small is mighty. Trends Biochem. Sci., 28, 534-540.
9. Murchison,E.P. and Hannon,G,J. (2004) miRNAs on the move: MiRNA biogenesis and the RNAi machinery. Curr. Opin. Cell. Biol., 16, 223-229.
10. He,Z. and Sontheimer,E.J. (2004) 'siRNAs and miRNAs': A meeting report on RNA silencing. RNA, 10, 1165-1173.
11. Lai,E.C. (2003) microRNAs: Runts of the genome assert themselves. Curr. Biol., 13, R925-R936.
12. Reinhart,B.J., Weinstein,E.G., Rhoades,M.W., Bartel,B. and Bartel,D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
13. Lee,R.C., Feinbaum,R.L. and Ambros,V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
14. Doench,J.G. and Sharp,P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
15. Kiriakidou,M., Nelson,P.T., Kouranov,A., Fitziev,P., Bouyioukos,C., Mourelatos,Z. and Hatzigeorgiou,A. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev., 18, 1165-1178.
16. Lai,E.C. (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nature Genet., 30, 363-364.
17. Boutla,A., Delidakis,C. and Tabler,M. (2003) Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes. Nucleic Acids Res., 31, 4973-4980.
18. Adai,A., Johnson,C., Mlotshwa,S., Archer-Evans,S., Manocha,V., Vance,V. and Sundaresan,V. (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res., 15, 78-91.
19. Lai,E.C., Tomancak,P., Williams,R.W. and Rubin,G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol., 4, R42.
20. Lim,L.P., Lau,N.C., Weinstein,E.G., Abdelhakim,A., Yekta,S., Rhoades,M.W., Burge,C.B. and Bartel,D.P. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev., 17, 991-1008.
21. Enright,A.J., John,B., Gaul,U., Tuschl,T., Sander,C. and Marks,D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, R1.
22. John,B., Enright,A.J., Aravin,A., Tuschl,T., Sander,C. and Marks,D.S. (2004) Human MicroRNA Targets. PLoS Biol., 2, e363.
23. Bartel,D.P. and Chen,C.Z. (2004) Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs. Nature Rev. Genet., 5, 396-400.
24. Carrington,J.C. and Ambros,V. (2003) Role of microRNAs in plant and animal development. Science, 301, 336-338.
25. Brennecke,J., Hipfner,D.R., Stark,A., Russell,R.B. and Cohen,S.M. (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25-36.
26. Brennecke,J. and Cohen,S.M. (2003) Towards a complete description of the microRNA complement of animal genomes. Genome Biol., 4, 228.
27. Hofacker,I.L., Fontana,W., Stadler,P.F., Bonhoeffer,S., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte f. Chemie, 125, 167-188.
28. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
29. Serra,M.J. and Turner,D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.