Vir-Mir db: Prediction of viral microRNA candidate hairpins

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Li, Sung Chou ^a   Shiau, Cheng Kai ^b   Lin, Wen Chang ^a,b  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; VIRUS RNA;

3' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; GENE STRUCTURE; GENE TARGETING; GENETIC IDENTIFICATION; HUMAN; INTERNET; NONHUMAN; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; RICE; RNA HYBRIDIZATION; RNA SEQUENCE; SENSITIVITY ANALYSIS; TAXONOMY; VIR MIR DATABASE; VIRUS CELL INTERACTION; VIRUS GENOME; ZEBRA FISH;

3' UNTRANSLATED REGIONS; ANIMALS; DATABASES, NUCLEIC ACID; GENOME, VIRAL; HUMANS; INTERNET; MICE; MICRORNAS; OPEN READING FRAMES; RATS; RNA, VIRAL; SEQUENCE ANALYSIS, RNA; SOFTWARE; USER-COMPUTER INTERFACE;

ARABIDOPSIS; DANIO RERIO; RATTUS; VIR;

EID: 38549083644     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm610     Document Type: Article

References (23)

1. Bartel, D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. 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-D144.
3. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
4. Chen, X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303, 2022-2025.
5. Olsen, P.H. and Ambros, V. (1999) The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol., 216, 671-680.
6. Johnson, S.M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D. et al. (2005) RAS is regulated by the let-7 microRNA family. Cell, 120, 635-647.
7. Megraw, M., Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Res. (Database issue):D149-155.
8. 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-D139.
9. Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA, 12, 192-197.
10. Bennasser, Y., Le, S.Y., Yeung, M.L. and Jeang, K.T. (2004) HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology, 1, 43.
11. Pfeffer, S., Zavolan, M., Grasser, F.A., Chien, M., Russo, J.J., Ju, J., John, B., Enright, A.J., Marks, D. et al. (2004) Identification of virus-encoded microRNAs. Science, 304, 734-736.
12. Hsu, P.W., Lin, L.Z., Hsu, S.D., Hsu, I.B. and Huang, H.D. (2007) ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res. 35, D381-D385.
13. Li, S.C., Pan, C.Y. ad Lin, W.C. (2006) Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics, 7, 164.
14. Grad, Y., Aach, J., Hayes, G.D., Reinhart, B.J., Church, G.M., Ruvkun, G. and Kim, J. (2003) Computational and experimental identification of C. elegans microRNAs. Mol. Cell, 11, 1253-1263.
15. Lai, E.C., Tomancak, P., Williams, R.W. and Rubin, G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol., 4, R42.
16. Berezikov, E., Guryev, V, van de Belt, J., Wienholds, E., Plasterk, R.H. and Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21-24.
17. Cullen, B.R. (2004) Transcription and processing of human microRNA precursors. Mol. Cell, 16, 861-865.
18. Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M.J., Tuschl, T., van Nimwegen, E. and Zavolan, M. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics, 6, 267.
19. Kruger, J. and Rehmsmeier, M. (2006) RNAhybrid: MicroRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
20. Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10 1507-1517.
21. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, L, Gunsalus, K.C. et al. (2005) Combinatorial microRNA target predictions. Nat. Genet., 37, 495-500.
22. Du, T. and Zamore, P.D. (2005) microPrimer: The biogenesis and function of microRNA. Development, 132, 4645-4652.
23. Aravin, A.A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J. and Tuschl, T. (2003) The small RNA profile during Drosophila melanogaster development. Dev. Cell, 5, 337-350.