Post

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

Ragnar {Groot Koerkamp}

@curiouscoding.nl

27 Mar 2025

And some more: - edit graph - cubic DP (as N&W originally introduced it) + quadratic DP (as fixed by many others) - cost models

Ragnar {Groot Koerkamp}

@curiouscoding.nl

See them in action here :) Although I may have to split the large ones so they go part-by-part. curiouscoding.nl/posts/pairwi...

curiouscoding.nlA History of Pairwise AlignmentTable of Contents 1 A Brief History 1.1 A*PA 1.2 A*PA2 1.3 Overview 2 Problem Statement 3 Alignment types 4 Cost Models 4.1 Minimizing Cost versus Maximizing Score 5 The Classic DP Algorithms 6 Linear...

27/3/25, 4:30 pm0 reposts5 likes

Ragnar {Groot Koerkamp}

@curiouscoding.nl

27 Mar 2025

Happy to get suggestions for improving them btw :)

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

It's been very cool to watch the content on your site grow. I've been dabbling with some alignment adjacent things and your posts have been invaluable.

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

Question on semi-global alignment - where did you find / come up with the names of "overlap", "extension", etc? I'd always thought of all of those as just variants of semi-global.

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

My basis for what is semi-global is coming from only two sources though. This set of slides from @robp.bsky.social rob-p.github.io/CMSC423_S20/... And the source code for parasail.

rob-p.github.iorob-p.github.io

Rob Patro

@robp.bsky.social

1 Apr 2025

So, in general, the terminology here has become hopelessly messy. Semi-global has come to stand in for an entire family of types of alignments. Ends-free is nice, but there are restrictions to it to specify which specific ends are allowed to be free. 1/3

Ragnar {Groot Koerkamp}

@curiouscoding.nl

27 Mar 2025

Asking the right questions there :") The semi-global fig is based on an earlier fig I did with Pesho, but redone to have a consistent style. The names are mostly from the WFA repo, and then I did a bit of freedom on top of that 1/ x.com/peshotrie/st...

x.comx.com