Module 7: Molecular Computing with RNA Sequences

 

RNA Structure, Ribosomal and Transfer RNA

transcriptional control module 7 contents Intron/Exon Boundary Sequences back to the index of modules


  • Secondary structures of RNA: RNA is single-stranded in its native state. It can hybridize intramolecularly through hydrogen bonds between A and U residues and C and G residues resulting in stem and loop type of structures. An excellent site for RNA secondary structure prediction is operated by Michael Zuker at Rensselaer Palytechnic Institute (Mfold Server - DNA input and Mfold Server - RNA input)

  • Transfer RNA: (Figure of tRNA Bound to ATP) One can search for tRNA genes in genomic DNA or RNA sequences by using the tRNAscan-SE program.

  • Ribosomal RNA: A compilation of ribosomal RNA's (rRNA) from both prokaryotic and eukaryotic organisms can be found at the lsu rRNA Database (large sub units) and the ssu rRNA Database (small sub units). The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. Also, 5S rRNA sequences can be accessed from the 5S rRNA Database either through a listing of prokaryotes and eukaryotes and/or based on a taxonomic classification.

  • RNA Genie: This program locates novel RNA genes based on the premise that all stable, functional RNAs share common structural elements and that sequences corresponding to these elements would occur preferentially in RNA genes. It employs six structural parameters unique to RNA genes such as the calculated free energy of intramolecular folding etc.


transcriptional control module 7 contents Intron/Exon Boundary Sequences back to the index of modules

| Return to SWBIC home |

The Southwest Biotechnology and Informatics Center WWW server is located at "http://www.swbic.org/".
Please send comments and suggestions to: [email protected]
SWBIC 2001