BIT 569 : RNA Purification and Analysis
Course Instructor: Sivamani
Elumalai
Librarian: Eleanor Smith
I. The Basics
An RNA
Structure Primer
http://www.rnabase.org/primer/
Basics of RNA Synthesis and Splicing
http://web.indstate.edu/thcme/mwking/rna.html
Article: RNA: Networks & Imaging
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1681517
II. Methods and Protocols
RNA
protocols
http://www.protocol-online.org/prot/Molecular_Biology/RNA/
Website collection
of 100s of protocols related to RNA and other topics.
Current Protocols—electronic book
http://www.lib.ncsu.edu/cgi-bin/proxy.pl?server=www.mrw2.interscience.wiley.com/cp/cpmb/cpmb_contents_fs.html
Go
to Chapter 4: Preparation and Analysis of RNA
III. Organizations and Forums
RNA forums
http://www.molecularstation.com/rna/
NCSU
RNA biology group
www.ncsu.edu/cbirna
IV. Mega Sites, Link Collections
RNA World WebSite
http://www.imb-jena.de/RNA.html
Collection of extensive and high quality links related to many different aspects
of RNA
M. Zuker – Research: Algorigthms & Thernmodynamcs for Nucleic Acid
Folding, Hybridization & Melting
Point Prediction
http://frontend.bioinfo.rpi.edu/zukerm/cgi-bin/rna-index.cgi
Large collection of RNA related tools and links
V. Tools
Molecular Calculator
http://www.ambion.com/techlib/Documents.html?fkResSxn=10&fkSubSxn=28
RNA RNA hybridization prediction
http://www.unc.edu/~starmer/free2bind/
Global Computational Resources for Bioinformatics Research:
Collection of
tools for RNA RNA Structure Prediction/Visualization
http://www.bioinformatics.utep.edu/BIMER/tools/rnaStructure.html
includes:
Mfold:predict
RNA secondary structure solely on the thermodynamic model
pknotsRG:parallels
Mfold and it can predict pseudoknots
PKNOTS:uses
a dynamic algorithm to predict RNA secondary structures
KineFold:uses ab initio menthod
to predict RNA structure, including pseudoknots
PseudoBase:a
database of known pseudoknots across many species
PseudoViewer:used
to view RNA structure predicted from other programs
RNAMovies 2.0.4
http://bibiserv.techfak.uni-bielefeld.de/rnamovies/
Sequential
Animation of RNA secondary structure including pseudoknots and entangled
helices.
RNAMovies is a system for the visualization of RNA secondary structure spaces,
i.e. multiple sets of secondary structure data. RNAMovies has been integrated
into the following bioinformatics tools:
- RNAshapes RNA
analysis tool
- pknotsRG RNA
folding and thermodynamic matching
- KineFold folding kinetics of RNA
sequences including pseudoknots
- paRNAss Prediction
of Alternating RNA Secondary Structures(not longer supported)
RNA secondary structure prediction
http://www.genebee.msu.su/services/rna2_reduced.html
Comparative RNA Web Site
http://www.rna.ccbb.utexas.edu/
Need to register (free)
Disseminates
information about RNA structure and evolution that has been determined using
comparative sequence analysis. Presents both raw (sequences, structure models,
metadata) and processed (analyses, evolution, accuracy) data. Types of
data, information, and modes of presentation include:
- RNA sequences
- RNA structure
- comparative sequence analysis
- RNA evolution
- accuracy
- RNA function
- database/metadata
- presentation
- secondary struture diagrams
RNAMap (secondary structure Java applet)
VI. Databases
The Structural Classification of RNA (SCOR)
http://scor.lbl.gov/
A database designed to provide a comprehensive perspective
and understanding of RNA motif structure, function, tertiary interactions
and their relationships.
RNABase
http://www.rnabase.org
RNABase offers access to a relational database containing
data about all publicly available RNA structures using a web driven interface.
RNABase provides complete conformational maps for each structure.
Nucleic Acid Database
http://ndbserver.rutgers.edu/index.html
A repository of three-dimensional structural information about nucleic
acids
Includes:
RNA
Viewer View RNA 2-dimensional structure using the RNAView program.
2D structure is fully annotated according to Leontis and Westhof (2001) RNA, 7, 499-512.
Transterm
http://uther.otago.ac.nz/Transterm.html
A
database of mRNA sequences and regulatory elements. provides access
to mRNA sequences and associated regulatory elements. The mRNA sequences
are derived from all gene sequence data in Genbank, including complete genomes,
divided into putative 5' UTRs and 3' UTRs, initiation and termination regions
and the full CDS sequences.
VI. Animations
Transcription
animation
http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html
Transcription
http://www.johnkyrk.com/DNAtranscription.html
Protein synthesis
http://www.biostudio.com/demo_freeman_protein_synthesis.htm
Whole collections of animations
http://science.nhmccd.edu/biol/bio1int.htm
http://vcell.ndsu.nodak.edu/animations/home.htm
http://www.dnalc.org/ddnalc/resources/animations.html
VII. Housekeeping
Lab reports
http://www.ncsu.edu/labwrite/index_labwrite.htm
Class evaluations
https://classeval.ncsu.edu
Librarian Contact Information
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