Robert Vaser
Robert Vaser
Hi Ilia, unfortunately the memory complexity is quadratic (O(graph_length * sequence_length)). We might add banded alignment which should facilitate the memory consumption. If your input is huge, you could try...
@ekg, does this approach guarantee optimal alignments?
Thanks for the clarification, I'll think about if the scope of changes is worth exploring.
Hi Paolo, I'll fix this as soon as possible. Best regards, Robert
Unfortunately, this feature is not implemented and at the moment I do not have the time to add it. It is well described in the second POA paper if you...
Sure, go ahead :)
Hello @SoapZA, I have heard of Meson before and am looking forward for your PR. When I get the time, I might add it to other submodules for easier integration....
There is a branch `dna_dev` which implements some kind of DNA support, but I do not have the time at the moment to deal with it properly.
If I recall correctly, you have been testing nucleotide-protein alignments but I am not sure what was the outcome. Sword was developed for protein-protein search only, and I would need...
You can also check out https://github.com/ivujevic/tachyon, much faster aligner which supports DNA sequences.