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Published 20 hours ago • verified publisher icon torognes

Improve multiple sequence alignment

Open torognes opened this issue 7 years ago • 3 comments

The multiple sequence alignment algorithm used in VSEARCH, the centre-star method, is rather simple. Consider implementing a better algorithm.

As a start, unaligned residues to the left of the first residue in the centre sequence could be right-aligned instead of left-aligned.

torognes avatar Dec 05 '16 07:12 torognes

Dr. Rognes and the VSEARCH team,

Do you have any update about this ticket? In particular, there is a bug in Clustering where the consensus sequence given for a cluster can sometimes be incorrectly trimmed in version 2.14.2. Has this bug been fixed in version 2.21 yet? Thanks!

yctai105 avatar Jan 02 '23 05:01 yctai105

I don't have any updates on this issue, unfortunately.

I was not aware that there was a bug related to consensus sequences in version 2.14.2. Could you give some more details? Do you have an example that shows the problem?

torognes avatar Jan 02 '23 09:01 torognes

So, the methods for doing multiple sequence alignments and consensus sequences have not been changed since version 2.14.2?

I am not sure if I am able to find an example for this bug, since it sometimes happened, but not always. I can try to find it, and let you know. Meanwhile, may I suggest that you to test and compare the consensus sequences using different datasets with those from USEARCH/Clustering? This way, you may find the issues quickly on your own.

yctai105 avatar Jan 02 '23 17:01 yctai105