Before using Sticky finder or Sticky finder counter, please make sure to download fasta.py and expSS_score.py
Sticky finder:
A python program that searches for the complementary sequences with a minimum length of 6 nts (default) between identical or non-identical transcripts.
Usage: modify the relevant parameters (i.e. RNA sequence of interest, RNA secondary structure in dot-bracket format, and name of the output files) inside sticky_finder_v3.py, then run sticky_finder_v3.py in a python shell (3.7 and above).
Output format: it produces two files. File1 in the script contains inverted repeats and palindromes. File2 has sense-antisense sequences.
Sticky finder counter:
A python program that counts the number of complementary sequences with a minimum length of 6 nts (default) and a user-defined %GC content, with the fasta file as an input.
Usage: sticky_finder_v3_counter.py fasta_file_randonmized_seqs GC%threshold of the complementary sequences
Output format: transcript name,gene name,sequence length,total # of palindromes,total # of inverted repeats,total number of sense-antisense sequences
UPDATE (03/10/2025): We have developed a graphical user interface (GUI) based on the Python scripts "sticky_finder_v3.py" and "sticky_finder_v3_counter.py". The application, "Sticky Finder.exe," can be run locally without the need to preinstall Python or any additional scripts.
For more details, please refer to: Sticky Finder Application Guide v1.pdf.