IconThe RNase P Database


Key to available file types, links & labels

Seq RNA sequence (in Genbank format). Displays in your browser as text, directly readable by most sequence editors.
CT

RNA secondary structure in Connect Format w/o pseudoknots. This format can be used by most RNA secondary structure drawing programs such as LoopDloop (Mac), RNAvis (PC/Unix) or XRNA (Unix). Basepairings that create pseudoknots are not included in these files - therefore, P4, P6, and P21 are not present.

Although not part of the definition of this file type, the first line starts (after the sequence length) with "ENERGY=0" so that RNA vis will recognise it properly.

CT2 RNA secondary structure in Connect format w/ pseudoknots. ".ct2" files are identical to the ".ct" files (above), except that pseudoknots are allowed. This means that most (all?) RNA secondary structure drawing programs can not properly use these files. However, more advanced analytical tools can sort these out properly, and all the basepairs are there!
RNAML

RNA secondary structure in RNAML format. This is the evolving XML file format developed by the RNA Society to address issues of RNA informatics that are not handled well (or at all) by GenBank or PDB data structures. Information about RNAML, the DTD, samples files, etc, can be found at http://www.smi.stanford.edu/projects/helix/RNAML/

The RNAML files on this database are, at present, very-much bare-bones, with the absolute minimum of information: just sequence and secondary structure. If RNAML is adopted by the community, I hope to move essentially everything to RNAML format.

PDF
old PDF

RNA secondary structures are available in Adobe Acrobat (.pdf) format. These are displayed directly in the window of modern web browsers, or can be saved and displayed/printed with Adobe Acrobat Reader. PDF links in green are based on the curent structure model. PDF links in grey are older images.
Protein Protein sequence (in GenBank format). Displays in your browser as text, directly readable by most sequence editors.

Species

The names of the species in the database are linked to the NCBI/Entrez Taxonomy database.
X12345 This is a Genbank accession number, linked to the original sequence reord at NCBI/Entrez.

citation

The text of most of the citation listings are linked to the Medline record for that paper via NCBI/Entrez.

PDB

Protein Database format. These are text files that can be read directly by most 3D molecular modeling or visualization programs. The Chime plug-in will let you veiw these directly in your browser window.

Kin

Kinemage format. This is a labeled, indexed 3D format for the viewing program MAGE.
Under construction Indicates information that has not been released and/or have been released and will be posted soon, or information in need of updating.


Last updated by JWBrown
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