E-RNAi: A web application for the multi-species design of RNAi reagents-2010 update

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Horn, Thomas ^a   Boutros, Michael ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA; DOUBLE STRANDED RNA; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS;

ACYRTHOSIPHON PISUM; AEDES AEGYPTI; ANOPHELES GAMBIAE; ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER INTERFACE; COMPUTER PROGRAM; DROSOPHILA; GENOME; MATHEMATICAL ANALYSIS; NUCLEOTIDE SEQUENCE; ORGANISM; PREDICTION; PRIORITY JOURNAL; RNA INTERFERENCE; SCHMIDTEA MEDITERRANEA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VALIDATION PROCESS; WEB BROWSER; ANIMAL; CHEMISTRY; GENE SILENCING; GENOMICS; HUMAN; INTERNET;

ANIMALS; GENE KNOCKDOWN TECHNIQUES; GENOMICS; HUMANS; INDICATORS AND REAGENTS; INTERNET; RNA INTERFERENCE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA; SOFTWARE;

ACYRTHOSIPHON PISUM; AEDES AEGYPTI; ANOPHELES GAMBIAE; CAENORHABDITIS ELEGANS; SCHMIDTEA MEDITERRANEA;

EID: 77954304698     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq317     Document Type: Article

References (24)

1. Boutros,M. and Ahringer,J. (2008) The art and design of genetic screens: RNA interference. Nat. Rev. Genet., 9, 554-566.
2. 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.
3. Chapman,E.J. and Carrington,J.C. (2007) Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet., 8, 884-896.
4. Clemens,J.C., Worby,C.A., Simonson-Leff,N., Muda,M., Maehama,T., Hemmings,B.A. and Dixon,J.E. (2000) Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl Acad. Sci. USA, 97, 6499-6503.
5. 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.
6. 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.
7. Kulkarni,M.M., Booker,M., Silver,S.J., Friedman,A., Hong,P., Perrimon,N. and Mathey-Prevot,B. (2006) Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nat. Methods, 3, 833-838.
8. Anderson,E.M., Birmingham,A., Baskerville,S., Reynolds,A., Maksimova,E., Leake,D., Fedorov,Y., Karpilow,J. and Khvorova,A. (2008) Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA, 14, 853-861.
9. Birmingham,A., Anderson,E.M., Reynolds,A., Ilsley-Tyree,D., Leake,D., Fedorov,Y., Baskerville,S., Maksimova,E., Robinson,K., Karpilow,J. et al. (2006) 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199-204.
10. Ma,Y., Creanga,A., Lum,L. and Beachy,P.A. (2006) Prevalence of off-target effects in Drosophila RNA interference screens. Nature, 443, 359-363.
11. Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nat Biotechnol., 22, 326-330.
12. Shah,J.K., Garner,H.R., White,M.A., Shames,D.S. and Minna,J.D. (2007) sIR: siRNA information resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. BMC Bioinformatics, 8, 178.
13. Wang,X., Varma,R.K., Beauchamp,L., Magdaleno,S. and Sendera,T.J. (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res., 37, e152.
14. Echeverri,C.J., Beachy,P.A., Baum,B., Boutros,M., Buchholz,F., Chanda,S.K., Downward,J., Ellenberg,J., Fraser,A.G., Hacohen,N. et al. (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat. Methods, 3, 777-779.
15. Henschel,A., Buchholz,F. and Habermann,B. (2004) DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res., 32, W113-W120.
16. Huesken,D., Lange,J., Mickanin,C., Weiler,J., Asselbergs,F., Warner,J., Meloon,B., Engel,S., Rosenberg,A., Cohen,D. et al. (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol., 23, 995-1001.
17. Tafer,H., Ameres,S.L., Obernosterer,G., Gebeshuber,C.A., Schroeder,R., Martinez,J. and Hofacker,I.L. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol., 26, 578-583.
18. Arziman,Z., Horn,T. and Boutros,M. (2005) E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res., 33, W582-W588.
19. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
20. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
21. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
22. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
23. Hofacker,I.L. (2009) RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics, Chapter 12:Unit12 12.
24. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.