RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database
| Submit structures
|The RNA Secondary Structure and Statistical
Release 2.0 May 2008. New features and modifications:
Release 1.3 Jan 2007. New features and modifications:
- Search by RNA sequence was added. Any pattern sequence using IUPAC codes is allowed.
- FASTA format was aded for download and view.
- The internal files are stored in CT format. This is better for duplexes that contain more than one sequence.
- The data was updated, and a lot more data from publically available databases was obtained.
- data from Rfam was studied family by family
- data from Pseudoviewer was removed because of reliability issues
- data from NDB was added, which is not included in PDB
- an issue with the PDB data is that there is no clear field that gives the RNA type and the organism. The RNA type is set to unknown for now, we thought it's better than making mistakes, and we couldn't check everything manually for 1059 structures.
- Redundancy issue was solved. Now redundancy is solved by checking the sequences of the search results.
- Links to the external IDs were added where applicable.
- Now individual files can be downloaded in RNAML format as well.
- Once a search is performed, all files which fulfilled the specified criteria can be downloaded as one archive, in any of bpseq,
dot-parentheses, ct or RNAML formats. For now, the CRW data cannot be downloaded directly.
- On the analysis form, a checkbox to normalize for RNA type was added.
- More options for non-canonical base pairs on the search and analysis forms were added.
Release 1.1 Sep 2006. New features and modifications:
- The database has been reinstalled from scratch. The molecule ID's have been changed to better reflect their provenance. A new digit to the number has been added.
- Many more families (seeds) from Rfam have been added.
- The database has been reinstalled from scratch. As such, some molecule IDs have been modified.
- We fixed some errors which we found in some files coming from the PDB database.
- Complexes with more than one molecule have the boundary information written in the bpseq file now.
Also, the figures show a yellow dot for the 5' end of every molecule in the complex,
and a cyan dot for the 3' end of every molecule in the complex.
- The RNase P RNA structures are from the latest RNase P Database version: No. 12. The molecule names contain the full organism name and strain.
This makes it easier to find an RNase P RNA file from our database in the original RNase P Database. The partial information was also added in our database.
- The tmRNA files from tmRDB are the secondary structure files now, and not the structures extracted from the tertiary structures.
- Some errors in the figures have been fixed.
- The RNA sequence has been added into a database entry, for easier search for sequence and redundancy detection.
- A new field: DUPLICATE has been added in the MOLECULE table, and a redundancy check has been performed. If two entries have identical sequences,
one of them has DUPLICATE=No, and the other one has DUPLICATE=Yes. The latter also contains the ID of the former entry, in the COMMENTS
| Submit structures
For questions, comments, suggestions and bug reports, please contact:
2004-2008 BETA LAB - University of British Columbia