Online Tools and Links Used in Bio-Genetic research
PseudoViewer outstanding freeware for drawing RNA structures often used by this site.
National Center for Biotechnology Information, NCBI
ClustalW2 - a general purpose multiple sequence alignment program for DNA or proteins.
DNALC- Sequence Utilities
HIV sequence database
Kinefold request form (pknots)
The DINAMelt Server
RFAM-RNA families database of alignments and CMs
RNA World Website
Human mitochondrial genome database MITOMAP
Retroviruses
Viral RNA Structure Database
Human (Homo sapiens) Genome Browser Gateway
Vienna RNA Sequence Design- Search sequences that will fold into a predefined secondary structure
Vienna RNA Secondary Structure - Prediction Consensus Structures of Aligned Sequences
RNA Studio
BI Sources - Bioinfoindia.org
http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html
DNA formating tool
Tools - windows exe (Part of the Vienna Package)
Kinfold.exe -- predict RNA secondary structure
RNAfold.exe -- predict minimum energy secondary structures and pair probabilities
RNAalifold.exe -- predict the consensus structure of several aligned sequences
RNAeval.exe -- evaluate energy of RNA secondary structure
RNAinverse.exe -- inverse fold (design) sequences with predefined structure
RNAplot.exe -- RNA structure drawings in PostScript, SVG, or GML
RNAsubopt.exe -- complete sub optimal folding
RNAheat.exe -- calculate the specific heat (melting curve) of an RNA sequence
RNAdistance.exe -- compare secondary structures
RNApdist.exe -- compare base pair probabilities
RNAcofold.exe -- predict hybrid structure of two sequences
RNALfold.exe -- predict locally stable structure of long sequences
RNAplfold.exe -- compute average pair probabilities for local base pairs in long sequences
RNApaln.exe -- fast structural alignment of RNA sequences using string alignments
Data Files
http://www.ncbi.nlm.nih.gov/genomes/genlist.cgi?taxid=10239&type=5&name=Viruses
5' LTR HIV
Viroids 1435 genomesHDV 584 genomes
Introductory Power Point -RNA String Parsing