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mcfrith / last-genome-alignments

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Human self-alignments? #1

Open bioinformed opened 7 years ago

bioinformed commented 7 years ago

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.

mcfrith commented 7 years ago

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?

lijingbu commented 4 years ago

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