The RNase P Database help

Icon The RNase P Database

Key to available file types, links & labels

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

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.

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!

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.

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 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.

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 May 23, 2001 by JWBrown
RNase P Database home page

	RNA sequence (in Genbank format). Displays in your browser as text, directly readable by most sequence editors.
	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.
	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!
	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.
	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 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.
	Indicates information that has not been released and/or have been released and will be posted soon, or information in need of updating.