detect recombination breakpoints in a query sequence by comparing it against a reference set.

genostack commented 1 year ago

Thanks for this nice tool. In the documents ,it says "or to detect recombination breakpoints in a query sequence by comparing it against a reference set." , but how to use it in thid mode?

ArtPoon commented 1 year ago

Sorry, that text is misleading. It was meant to describe RDP itself, and not our open source re-implementation of RDP, which is unfortunately incomplete. I will amend.

ArtPoon commented 1 year ago

Amended README file. I will leave this issue open as a placeholder for further work, for now. I don't think it should be that difficult to implement...

ArtPoon commented 1 year ago

@SandeepThokala - I think this can be done with the following changes:

allow user to optionally input a second alignment of reference sequences (not query sequences)
- in other words, we currently have the user input an alignment of query sequences, and then the program is checking every subset of three sequences, i.e., {Q1, Q2, Q3}, {Q1, Q2, Q4}, {Q1, Q2, Q5}, etc.
- in this case, each sequence in the query set would be compared to two "parental" sequences in the reference set (R), i.e., {Q1, R1, R2}, {Q1, R1, R3}, ...

GopiGugan commented 11 months ago

@SandeepThokala to create a PR into dev

ArtPoon commented 9 months ago

Close issue upon merging PR #66

ArtPoon commented 3 weeks ago

Need to check that if user specifies a reference set of sequences, the Triplet containing two parent sequences from this ref set should only be checked for the third sequence (coming from the main input alignment) as the potential child of two reference sequences. In other words, we should not be doing three times the work, checking whether either of the two reference sequences is a child recombinant.

darrenpmartin commented 3 weeks ago

Scanning only triplets that contain two reference sequences and one query sequence is sensible but if the reference set contains only one parent - in such situations the recombination signal might still be detectable but only if you consider the references as possible recombinants. Does that make sense?

On Mon, Jun 10, 2024 at 9:26 PM Art Poon @.***> wrote:

Need to check that if user specifies a reference set of sequences, the Triplet containing two parent sequences from this ref set should only be checked for the third sequence (coming from the main input alignment) as the potential child of two reference sequences. In other words, we should not be doing three times the work, checking whether either of the two reference sequences is a child recombinant.

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PoonLab / OpenRDP

detect recombination breakpoints in a query sequence by comparing it against a reference set. #64