search

torognes / vsearch

Versatile open-source tool for microbiome analysis
Other
655 stars 122 forks source link

Improve multiple sequence alignment #218

Open torognes opened 7 years ago

torognes commented 7 years ago

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.

yctai105 commented 1 year ago

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!

torognes commented 1 year ago

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?

yctai105 commented 1 year ago

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.