Skip to content
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.

Sign up for GitHub

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

Jump to bottom

taxator: port RPA to protein sequences #26

Closed
fungs opened this issue Mar 13, 2015 · 3 comments
Closed

taxator: port RPA to protein sequences #26

fungs opened this issue Mar 13, 2015 · 3 comments
Labels
enhancement high priority

Comments

@fungs
Copy link
Owner

fungs commented Mar 13, 2015

Basically, the whole algorthm is independent of sequence type if a proper pairwise alignment algorithm and score is used. Therefore, it should be possible to run the same algorithm with protein sequences. I expect it to be somewhat slower than for nucleotide sequences because we cannot use the ultra-fast edit-score alignment algorithm in SeqAn.
@fungs
Copy link
Owner Author

fungs commented Mar 13, 2015

Reason for this: users are requesting the functionality with protein level aligners such as BlastX.

@fungs
Copy link
Owner Author

fungs commented Nov 4, 2016

We have a working implementation which needs some testing, still. Stay tuned.

@fungs
Copy link
Owner Author

fungs commented Oct 1, 2021

the protein space alignment algorithm has been fully implemented and will be contained in release 1.5

@fungs fungs closed this as completed Oct 1, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement high priority
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@fungs