A rapid method for detection of putative RNAi target genes in genomic data

Bioinformatics

Volumn 19, Issue SUPPL. 2, 2003, Pages

  Horesh, Yair ^a   Amir, Amihood ^a   Michaeli, Shulamit ^a   Unger, Ron ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

C.briggsae; C.elegans; Control mechanism; RNAi; Suffix tree

Indexed keywords

BASE PAIRING; CAENORHABDITIS ELEGANS; CONFERENCE PAPER; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE TARGETING; GENETIC ANALYSIS; GENOME; INVERTED REPEAT; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA DEGRADATION; SYNTENY;

RNA VIRUSES;

EID: 17244378534     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1063     Document Type: Conference Paper

References (24)

1. Amir, A., Landau, G., Keselman, D., Lewenstein, M., Lewenstein, N. and Rodeh, M. (2000) Text indexing and dictionary matching with one error. J. Algorithms, 37, 309-325.
2. Bernstein, E., Caudy, A.A., Hammond, S.M. and Hannon, G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363-366.
3. Blaxter, M. (1998) Caenorhabditis elegans is a nematode. Science, 282, 2041-2046.
4. Couzin, J. (2002) Breakthrough of the year: small RNAs make big splash. Science, 298, 2296.
5. Djikeng, A., Shi, H., Tschudi, C. and Ullu, E. (2001) RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs. RNA, 7, 1522-1530.
6. Eddy, S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
7. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
8. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E. and Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
9. Gusfield, D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge.
10. Hannon, G.J. (2002) RNA interference. Nature, 418, 244-251.
11. Heringa, J. (1998) Detection of internal repeats: how common are they? Curr. Opin. Struct. Biol., 8, 338-345.
12. Johnstone, J.L. (2000) Cuticle collagen genes. Expression in C.elegans. Trends Genet., 16, 21-17.
13. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
14. Lee, R.C. and Ambros, V. (2001) An extensive class of small RNAs in C.elegans. Science, 294, 862-864.
15. 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 C.elegans. Science, 294, 858-862.
16. Maeda, I., Kohara, Y., Yamamoto, M. and Sugimoto, A. (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol., 11, 171-176.
17. McCreight, E.M. (1976) A space-economical suffix tree construction algorithm. J. ACM, 23, 262-272.
18. Mullikin, J.C. and Ning, Z. (2003) The phusion assembler. Genome Res., 13, 81-90.
19. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R. and Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in C.elegans. Nature, 403, 901-906.
20. Shi, H., Djikeng, A., Mark, T., Wirtz, E., Tschudi, C. and Ullu, E. (2000) Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA. RNA, 6, 1069-1076.
21. Tabara, H., Sarkissian, M., Kelly, W.G., Fleenor, J., Grishok, A., Timmons, L., Fire, A. and Mello, C.C. (1999) The rde-1 gene, RNA interference, and transposon silencing in C.elegans. Cell, 99, 123-132.
22. th IEEE Symp on Switching and Automata 1-11.
23. Wesley, S.V., Helliwell, C.A., Smith, N.A., Wang, M.B., Rouse, D.T., Liu, Q., Gooding, P.S., Singh, S.P., Abbott, D. Stoutjesdijk, P.A. et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J., 27, 581-590.
24. Zuker, M. and Jacobson, A.B. (1998) Using reliability information to annotate RNA secondary structures. RNA, 4, 669-679.