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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
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A way to prefer closer exons in tandemly duplicated genes on the same strand #53

Closed melop closed 6 months ago

melop commented 6 months ago

I think this is related to a known issue. When we are dealing with tandemly duplicated genes on the same strand, miniprot could prefer more distant exons instead of the ones closer. The phenomenon can be visualized below: image

Some long introns would result in this case. I'm thinking, is it possible to give penalties to intron length, so that miniprot would prefer the alignment with the closest exons?

Ray

lh3 commented 6 months ago

You may increase -w to adjust the gap penalty during chaining.