Non optimal alignment

[marijnsanders]

Hi,

I have tried to align the sequences:

Name,Sequence
Seq1,GTGHKL
Seq2,GTGHKVL
Seq3,GTGPHKL
Seq4,GTGPHTHKL
Seq5,GTGTAHKL
Seq6,GTGAKHKL
Seq7,GTGKLHKL
Seq8,GTGVVHKL
Seq9,GTGHVKL

with varying gapopen and gapextend penalties it does not seem to return a satisfying result.

The result looks often not optimal and gaps can be removed to create a better alignment.

The code I have used uses:
biomsa.align(
mySequences,
{
gapopen: gapopen,
gapextend: gapextend,
// matrix: [[.....], [.....], ....],
method: 'auto',
type: 'auto',
gapchar: '-',
debug: false
})

What is the reason for these gaps and is there a way to optimize the alignment?
Thanks in advance,

[ppillot]

Thanks about that. Yes, you are right these alignments don't look good at all. I am aware of an issue with the part of the algorithm that aligns two multiple alignments together. I've spent some time investigating this and could not figure what is the root cause for that.
Unfortunately, I don't have the bandwidth at the moment to spend more time on this project. I am aware of aligners that rely on web assembly and could be a suitable alternative (Kalign has been compiled to web assembly for biowasm https://biowasm.com/documentation)

[marijnsanders]

Hi,

Thanks for the reply. I do understand. Will look into biowasm.

[ppillot]

Hi, I've made some progress with the alignments. Using your example, here is the result I got with version 0.3.3