Further Information and References

Introduction Spirin AS. Omnipotent RNA. FEBS Lett. 2002 Oct 23;530(1-3):4-8. PMID 12387857 S. Buckingham, "The major world of microRNAs," presented at Horizon Symposia Understanding the RNAIssance, 2003. http://www.nature.com/horizon/rna/background/micrornas.html NCBI's Databases for generic sequence information http://www.ncbi.nlm.nih.gov/ Meli M, Albert-Fournier B, Maurel MC. Recent findings in the modern RNA world. Int Microbiol. 2001 Mar;4(1):5-11. Review.: PMID: 11770821 Coding RNAs Virology sites for information on viruses: http://www.virology.net and links to viral information: http://www.cdc.gov NCBI's Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html Influenza Sequence Database at NCBI: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html and LANL http://www.flu.lanl.gov/ HIV Sequence Database: http://hiv-web.lanl.gov/content/hiv-db/combined_search/search Nucleic Acid Research viral genome databases: http://www.oxfordjournals.org/nar/database/subcat/5/18 Non-coding RNAs NONCODE database of non-coding RNAs: http://www.bioinfo.org.cn/noncode/index.htm Non-coding RNAs: tRNA Alberts B, Johnson A, Lewis J et al. (2002) Molecular Biology of the Cell, 4th edn. New York: Garland Science. (An online version of this book is available in the Entrez Books database) tRNA Compilation 2000: http://www.uni-bayreuth.de/departments/biochemie/trna/ The Genomic tRNA database: http://lowelab.ucsc.edu/GtRNAdb/ Compilation of mammalian mitochondrial tRNA genes: http://mamit-trna.u-strasbg.fr/ Organelle Genome Resources at NCBI: http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html GOBASE: http://gobase.bcm.umontreal.ca/ MITOMAP: http://www.mitomap.org/ tRNA Gene Prediction Program: tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/ Non-coding RNAs: rRNA Alberts B, Johnson A, Lewis J et al. (2002) Molecular Biology of the Cell, 4th edn. New York: Garland Science. (An online version of this book is available in the Entrez Books database) Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001 May 4;292(5518):883-96. PMID: 11283358 The European Ribosomal RNA Database: http://www.psb.ugent.be/rRNA/ 5S Ribosomal RNA Database: http://biobases.ibch.poznan.pl/5SData/ Prokaryotic 16S rRNA Signature Database: http://prion.bchs.uh.edu/16S_signatures/ Ribosomal Database Project (RDP-II): http://rdp.cme.msu.edu/index.jsp 16S and 23S Ribosomal RNA Mutation database: http://ribosome.fandm.edu/ Organelle Genome Resources at NCBI: http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html GOBASE: http://gobase.bcm.umontreal.ca/ Database of ribosomal crosslinks: http://www.molgen.mpg.de/~ag_ribo/ag_brimacombe/drc/ Other types of non-coding RNAs: tmRNA & IRES The tmRNA website: http://www.indiana.edu/~tmrna/ tmRDB: http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html Sarnow P, Cevallos RC, Jan E. Takeover of host ribosomes by divergent IRES elements. Biochem Soc Trans. 2005 Dec;33(Pt 6):1479-82.: PMID: 16246150 IRESdb: http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ IRESite: http://www.iresite.org/ Other types of non-coding RNAs: snRNA, snoRNA, gRNA, & SRP NONCODE ncRNA list of snRNA: http://www.bioinfo.org.cn/noncode/showclass.php?class=snRNA Methylation guide snoRNA database: http://lowelab.ucsc.edu/snoRNAdb/ Yeast snoRNA database: http://people.biochem.umass.edu/fournierlab/snornadb/main.php Plant snoRNA database: http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home snoRNAbase: http://www-snorna.biotoul.fr/ gRNA database: http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html Signal recognition particle database: http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html Non-coding RNA: RNA-mediated interference (RNAi) Nature Reviews RNAi collection [Online][date cited: July 29, 2007]: http://www.nature.com/focus/rnai/index.html Nature Reviews animation of the RNAi process: http://www.nature.com/focus/rnai/animations/index.html Nova ScienceNOW RNAi [Online][date cited: July 29, 2007]: http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html RNAi portal: http://www.ncbi.nlm.nih.gov/genome/RNAi/ NCBI Probe Database: http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe (see also Probe query tips) RNAi Codex (CSHL): http://codex.cshl.edu/scripts/newmain.pl The RNAi Consortium: http://www.broad.mit.edu/genome_bio/trc/ RNAi Resource (Ambion): http://www.ambion.com/techlib/resources/RNAi/ RNA@Elegansnet: http://c.elegans.tripod.com/RNAi.htm RNAi database (C. elegans): http://nematoda.bio.nyu.edu/cgi-bin/rnai/index.cgi Whitehead Algorithm: http://jura.wi.mit.edu/bioc/siRNAext/ EMBOSS Algorithm: http://bioweb.pasteur.fr/seqanal/interfaces/sirna.html RNAi portal: http://www.ncbi.nlm.nih.gov/genome/RNAi/ Other RNAi resources Costa FF. Non-coding RNAs: lost in translation? Gene. 2007 Jan 15;386(1-2):1-10. Review.: PMID: 17113247 Matzke MA, Matzke AJ. Planting the seeds of a new paradigm. PLoS Biol. 2004 May;2(5):E133. Review.: PMID: 15138502 RNA interference: historical overview and significance. Montgomery MK. Methods Mol Biol. 2004;265:3-21. Review.: PMID 15103066 Derivation and function of small interfering RNAs and microRNAs. Cullen BR. Virus Res. 2004 Jun 1;102(1):3-9.: PMID 15068874 MicroRNAs: small RNAs with a big role in gene regulation. He L, Hannon GJ. Nat Rev Genet. 2004 Jul;5(7):522-31. Review.: PMID 15211354 Non-coding RNA: Riboswitches, Aptamers, & Ribozymes Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature. 2006 Jun 29;441(7097):1167-71.: PMID: 16728979 Diagram of SELEX [Online][date cited: July 29, 2007]: http://www.molmed.uni-luebeck.de/T.%20Restle/selex.html Aptamer database: http://aptamer.icmb.utexas.edu/tables.php Sullenger BA, Gilboa E. Emerging clinical applications of RNA. Nature. 2002 Jul 1;418(6894):252-8.: PMID: 12110902 Chen X, Li N, Ellington AD. Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers. 2007 Apr;4(4):633-55.: PMID: 17443876 RNA Modification RNA Modification Database: http://medlib.med.utah.edu/RNAmods/ RNA Editing Web Site: http://dna.kdna.ucla.edu/rna/index.aspx RNA Structural Analysis Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39.: PMID: 11014182 Ignacio Tinoco, Jr. in Gesteland RF and Atkins JF (1993) The RNA World. Cold Spring Harbor Laboratory Press.: Alberts B, Johnson A, Lewis J et al. (2002) Molecular Biology of the Cell, 4th edn. New York: Garland Science. (An online version of this book is available in the Entrez Books database) Theimer CA, Blois CA, Feigon J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell. 2005 Mar 4;17(5):671-82.: PMID: 15749017 Comparative RNA Web Site: http://www.rna.ccbb.utexas.edu/ Wu H, Yang PK, Butcher SE, Kang S, Chanfreau G, Feigon J. A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III. EMBO J. 2001 Dec 17;20(24):7240-9.: PMID: 11743000 Lu D, Searles MA, Klug A. Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition. Nature. 2003 Nov 6;426(6962):96-100.: PMID: 14603324 Secondary Structure Prediction MFOLD: http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi RNA View secondary structure viewer: http://ndbserver.rutgers.edu/services/rna_viewer/ Vienna RNA Package: http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi Alifold: http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi SFold: http://www.bioinfo.rpi.edu/applications/sfold/srna.pl DINAMelt: http://www.bioinfo.rpi.edu/applications/hybrid/twostate-fold.php RNAstructure: http://rna.urmc.rochester.edu/rnastructure.html COVE/RNABOB/PKNOTs/ others: http://selab.wustl.edu/cgi-bin/selab.pl?mode=software RNAdraw: http://www.rnadraw.com/ Non-canonical Base Pair Database: http://prion.bchs.uh.edu/bp_type/ Michael Zuker's RNA page: http://www.bioinfo.rpi.edu/~zukerm/rna/ The bracket notation for RNA secondary structures [Online][date cited: July 29, 2007]: http://www.tbi.univie.ac.at/~ivo/RNA/bracket.html Structural databases and resources RNABase: http://www.rnabase.org NDB: http://ndbserver.rutgers.edu/ RCSB (PDB): http://www.rcsb.org/pdb/ MMDB: http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml SCOR: http://scor.lbl.gov Cn3D: http://0-www.ncbi.nlm.nih.gov.ilsprod.lib.neu.edu/Structure/CN3D/cn3d.shtml Base Pair Viewer: http://ndbserver.rutgers.edu/services/BPviewer/index.html Visualization and Analysis of 3D Structure World Index of Molecular Visualization Resources: http://molvis.sdsc.edu/visres/index.html Mc-Sym: http://www-lbit.iro.umontreal.ca/mcsym/ A few RNA sites to remember Comparative RNA Web Site: http://www.rna.ccbb.utexas.edu/ The RNA World: http://www.imb-jena.de/RNA.html Michael Zuker's RNA page: http://www.bioinfo.rpi.edu/~zukerm/rna/ RNABase: http://www.rnabase.org/ The RNA Webring: http://j.webring.com/t/RNA-WebRing The RNA Society: http://www.rnasociety.org/ Nucleic Acids Research: http://www.oxfordjournals.org/nar/database/cat/5 The journal RNA: http://www.rnajournal.org/