Citation: Wang F, Calvo-Roitberg E, Rembetsy-Brown J, Sousa J, Meda Krishnamurthy P, Lee J, Fang M, Green M, Pai A, Watts J. (2022). G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects (Nucleic Acids Research)
https://doi.org/10.1093/nar/gkac1108
This script scans an input fasta file for sequences that match or are complementary to the ASO sequence of interest.
python (v3.3.2)
In _ G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects_ we showed that antisense oligonucleotides (ASOs) that were carefully designed can still have off-target effects. This script scans an input fasta file containing multiple features and calculates a pairing score based on the provided position-specific score matrix (pssm) that can be customized according to the researchers needs.
An example of a pssm is provided here. Each column represents a base on the ASO and each row the matching nucleotide, thus, each cell is the assigned score for finding that nucleotide at a given ASO position.
usage: scanMotifs_summedScore.py [-h] [--pssm PSSM] [--fasta FASTA]
[--outname OUTNAME] [--distance DISTANCE]
[--minscore MINSCORE]
optional arguments:
-h, --help show this help message and exit
--pssm PSSM pssm for motif desired - REQ
--fasta FASTA fasta file to be searched (full path) - REQ
--outname OUTNAME name of output file (full path) - REQ
--distance DISTANCE amount of sequence to be used [full, X (nuc)]
--minscore MINSCORE minimum score to report (default = 10)
| Column Name | Description |
|---|---|
| feature | name of the feature used to blast the ASO |
| pssm_start | start of the feature targeted by the ASO |
| pssm_end | end of the feature targeted by the ASO |
| seq | targeted sequence |
| pssm_score | summed pairing score between the ASO and the feature |
| strand | strand used to calculate the score |