Script for detection of polypyrimidine tract (PPT) in intronic sequence
The script takes as standard in (stdin) a table of intron sequences. The 50 nt closest to the intron 3' splice site is enough. The table should be tab delimited and have two columns
- name, 2) sequence
The script will detect the PPT conforming to the rules set out in: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991248/ maximizing for length:
- Both 3' and 5' ends must be pyrimidines;
- No more than two contiguous purines are allowed;
- Every purine segment (length L<3) must be surrounded by at least 4L pyrimidines (this forces a minimum pyrimidine content greater than 2/3) distributed in a way that both upstream and downstream pyrimidine segments are of length greater or equal to L;
- T(GT)n stretches are allowed;
- Minimum length of 9nt, uridine content greater or equal to 5.
- If multiple qualifying PPT are found only report the one closest to 3' splice site (3'ss)