[xaa]

Alas, alignment is not in my area of expertise, nor of the people I know directly. I'm a heavy user, but not a developer of aligners (except a toy one). You could consider contacting Cole Trapnell or someone well known for making a widely used aligner and propose a collaboration, but that is a hard cold call. On the plus side, it means I probably wouldn't be your reviewer :) (but editors do sometimes get desperate...)

Your initial problem, if you frame it as the desire to simply enumerate all the degenerate sequences and loci, could be solved any number of ways as other commenters have mentioned. Probably I would reach first for a regex. But sure, no crime in learning to implement a new algorithm while also testing the limits of V8. Probably half of my grad school time was spent that way ;)

I think your best bet if you wanted to publish would be to find a use case for in-browser alignment. It would be hard to answer the obvious question, "why not server-side?" though. But who knows, people are somewhat often taking old bioinformatics algorithms and saying "but now you can do it on your phone!!". And they do publish.

But as for matching both speed and accuracy of state-of-the-art aligners with Javascript, it is my considered, scholarly opinion that you have no chance in hell. So you shouldn't present it that way. It would be unnecessary to compare (at least for speed) if you weren't making claims about speed.