Selected Applications

Many of these apps are used for internal research. They are, however, freely provided for download here with no claims made by RNAParse.

Tandem complement repeats of n=12,14,16,18,20.exe  
Example dnatcr.txt file  (~1 million bases)

Matches  {{{{{{N...}}}}}}, through {{{{{{{{{{N...}}}}}}}}}} where {} is a complement repeat: eg. ATCGAT.TAGCTA, AAAAAA.TTTTTT...

screenshot

Ribo-like frameshifting pseudoknot scanner  
 
Notes on usage of this demo:  
Create 1-2 files called DNA1, DNA2 of 80,000 nucleotides or less with no spaces or download those modifiable examples provided below. This scanner matches the structures listed here:
 ((((::[[[[))))::::::::::]]]]
 ((((::[[[[)))):::::::::]]]]  
 ((((::[[[[))))::::::::]]]] 
 ((((::[[[[)))):::::::]]]]

DNA Repeats.exe - Direct repeats of size 4-10

If you have problems running apps, or wish modified copies of these applications, email me at jlynn@acsalaska.net  

Test text files: DNA1 100k bp random DNA  
Test text files: DNA2 100k bp random DNA   -