Rna Parse

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) Right click and save.

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

 

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

Entropy- returns the Shannon Entropy of a text string placed into data.txt
data.txt - Right click and save.

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   -  

aaaaaaaaaaaaiii