Search parameters for flexible sequences - introns

[herber4]

Hi Danny,

Thanks for putting together such a cool program. I am working on mapping structures in introns using SHAPE experimental data, do you have any recommendations for search parameters, or do you still recommend using default parameters for SHAPEwarp? My sequences are ~1 kb, and introns tend to be fairly flexible. I test searched a single intron against a db of 8 different introns and only had one significant 20 bp hit.

Using this tool is experimental for us, we don't really know what to expect. Any insight is appreciated.

Best,

Austin Herbert

[dincarnato]

Dear Austin,

I am so terribly sorry but for some reason I have never received notification about this message. First of all, have you tried the new SHAPEwarp rewrite in Rust?

Please let me know if I can be of any help.

All the best, Danny