Rna Parse Database Notes

RNA Parse Database Notes

All data is freely available for research. Please cite: RNAParse.com James F. Lynn.
The database is very recently built (July 2009) and updated frequently with new material. Selected short pknots from the pseudobase site are included and renamed with a RP#0000 due to
convention (See notes section of the database for credits and additional information.)

Convert all U to T where applicable.

Bio-computational pseudoknots may or may not exist in nature. The purpose of this database is to help determine the specific properties that natural pseudoknots possess. Thus,
the computational methods used to discover new structures entered here are "possibility" structures and may or may not have gone further filtering via energy methods.
Structures that pass or fail energy models are denoted in the notes portion of the databases as: KSPOS or KSNEG, meaning they have passed "knot seeker" criteria for actually being pseudoknots.

We will be introducing statistical nt. analysis of stem-loop composition and new "reports" as a means of increased filtering of actual pknots as the database evolves.

If you are seeking specific structural data please contact us.

Perfect/Imperfect Tandem/Semi-Tandem Complement Repeats Database Notes

Available 3/2010: Perfect/Imperfect Tandem/Semi-Tandem Complement Repeats Database.
General form:


Availible 6/2010: Pknot Analysis Database. These are filtered-parsed pseudoknots using lingusitic methods that agree with minimal-energy models.