Welcome to the GenomeWeb
RNA Analysis and Databases
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These are a collection of RNA analysis and database sites.

[info] The rRNA WWW server
[info] The RNA World
[info] Guide RNA (gRNA) database
[info] The U-insertion/deletion Edited Sequence Database
[info] Compilation of tRNA sequences and sequences of tRNA genes
[info] Signal Recognition Particle Database (SRPDB)
[info] Small RNA database
[info] RNA secondary structure prediction
[info] mfold - predict RNA secondary structures
[info] Michael Zuker's RNA page
[info] 16S and 23S Ribosomal RNA Mutation Databases (16SMDBexp and 23SMDBexp)
[info] The Scottish RNA Club

Detailed information on the above options

The rRNA WWW server
The rRNA WWW server provides several services regarding the ribosomal RNA including aligned sequences with secondary structure information.

The RNA World
The RNA World at IMB Jena holds links to RNA related topics.

Guide RNA (gRNA) database
gRNA is a post-transcriptional editing template found in some protozoa.

The U-insertion/deletion Edited Sequence Database
This database contains sequences of mitochondrial genes and cryptogenes from kinetoplastid protozoa. Edited mRNA sequences and translated amino acid sequences are also provided.

Compilation of tRNA sequences and sequences of tRNA genes
This compilation contains 3279 sequences of tRNAs and tRNA genes covering the literature up to December 1996.

Signal Recognition Particle Database (SRPDB)
A tool in the study of the structure and function of signal recognition particle (SRP). Il provides annotated SRP RNA sequences from eukaryotes and archaea, phylogenetically ordered and aligned with their bacterial equivalents

Small RNA database
Small RNAs are broadly defined as the RNAs not directly involved in protein synthesis.

RNA secondary structure prediction
ALGORITHM:

If there's no significant multiple alignment, including the sequence, that you interest, then the secondary structure is built, using only the energy model (just the potential energy of the system is minimized), but very often such method will give unreliable results.

If a multiple alignment is given, then information on conservative positions in it and compensation exchanges in some of those will be used

into the resulting secondary structure.

mfold - predict RNA secondary structures
Scondary structure prediction for RNA is fundamentally different from three dimensional molecular modeling.

The method described here uses energy rules developed by Turner and colleagues. Negative stabilizing energies are assigned to the stacking of base pairs in helical regions, and to single bases that stack at the ends of helical regions. Otherwise, destabilizing energies are assigned to bulge, interior, hairpin and multi-branched loops. The energies of base stacking and the destabilizing loops are assumed to be additive in computing the overall energy. Pseudoknots, are not permitted in secondary structure calculations.

Michael Zuker's RNA page

16S and 23S Ribosomal RNA Mutation Databases (16SMDBexp and 23SMDBexp)
The 16S Ribosomal RNA Mutation Database (16SMDB), currently at Franklin and Marshall College, consists of an annotated list of 233 alterations distributed over 134 positions in 16S ribosomal RNA from Escherichia coli. Mutated positions are arranged in order beginning with the 5' end of 16S rRNA and ending with the 3' end. Phenotypes associated with each alteration are briefly described and designated as to whether the phenotypes were detected in vivo or in vitro . Appropriate references are provided for each alteration.

The 23S Ribosomal RNA Mutation Database (23SMDB), currently at Franklin and Marshall College, consists of an annotated list of 235 alterations distributed over 129 positions in 23S ribosomal RNA from Escherichia coli.

The Scottish RNA Club
The aim of the club is to enable RNA workers in Scotland (and anyone else interested) to meet informally, and communicate via Internet.

Any Comments, Questions? Support@hgmp.mrc.ac.uk