-
Notifications
You must be signed in to change notification settings - Fork 16
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Use information from conserved introns #60
Labels
enhancement
New feature or request
Comments
Thanks. GeMoMa is doing something similar. However, it is difficult to use position-specific scoring along the protein sequence (easier along the genome sequence), and it is also difficult for users to extract the information. |
OK, thanks - I was not aware of GeMoMa. Perhaps a script for postprocessing of miniprot alignments might achieve a similar result. I might try this. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Dear @lh3 ,
Thanks for developing miniprot. I have been trying it out & it is extremely useful.
I had an idea for a possible enhancement... it would be very interesting to be able to provide known intron positions (within the query protein sequences), and have a bonus score for alignments that include these. Many introns are very well conserved across species in terms of position and phase.
I'm not sure how this information would be best provided to miniprot, perhaps as a bed file or gff with protein coordinates & phase info showing how each query protein sequence is subdivided into exons.
Best wishes
Matt
The text was updated successfully, but these errors were encountered: