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Welcome to the GenomeWeb RNA Analysis and Databases Search for:

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

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.

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

• RNA related publications of Michael Zuker
• Lectures on RNA Secondary Structure Prediction (incomplete)
• Thermodynamic considerations & rules for RNA folding
• RNA folding and search software
• Three dimensional RNA modeling
• RNA secondary structure display software
• RNA Databases
• The RNA World at IMB Jena
• Computational Structural Biology at the NIH
• Books, Journals, Societies & Meetings

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.