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Published 20 hours ago • verified publisher icon mcfrith

Human self-alignments?

Open bioinformed opened this issue 7 years ago • 2 comments

Does last have the ability to efficiently compute self-alignments? lastz has a mode specifically for this, but I was hoping to be able to replicate that more rapidly with last.

bioinformed avatar Jun 02 '17 18:06 bioinformed

Unfortunately last does not (yet) have such a mode. Maybe one day, but probably not in the near future. Naive self-alignment with last is not catastrophically inefficient, at least.

I'll also mention that it's unclear to me what genome self-alignment should ideally do. Find all pairs of paralogous sequences, no matter how ancient their common ancestor? Align all pairs of Alus - surely not?

mcfrith avatar Jun 05 '17 02:06 mcfrith

It might help to detect segmental duplications. Lastz does have a self-alignment and dot plot function.

lijingbu avatar Jun 01 '20 02:06 lijingbu