I am calculating the percent identity between hundreds of MSAs. I was using the clustal executable for mac to do so with the following code:
./clustal-omega-1.2.3-macosx -i jock.fasta --percent-id --distmat-out jock.fasta.test -o jock.clustal --full
However, when I double check against the website the percent identity values are really different using the same sequence.
For example here is some output from the command line:
D_GUNUNGCOLA.Jockey 100.000000 89.201374
D_elegans.Jockey 89.201374 100.000000
And here it is from the website:
1: D_elegans.Jockey 100.00 99.63
2: D_GUNUNGCOLA.Jockey 99.63 100.00
This is just small example of a much larger pattern.
The sequences yielding this result are here: https://pastebin.com/wTrWYxqy
The -- are because these two sequences are part of a larger MSA.
Any insight is appreciated, I don't have time to enter each MSA into the website and wait for the results but it seems to be much more accurate? What I would like to do is recreate the website results on the command line.
1 answer
You don't have the most recent program version (1.2.3 vs 1.2.4). As already pointed out, it is possible that you are using different options locally.
I tested your sequences after I wrote the above paragraph, and also get the same result as you did locally. While everything I said above stands, it is possible that there is some kind of a bug here, as the identity between the two sequences is clearly >99% and is correctly reported by the web version.
i'm sure that 10% in sequence divergence is whats different between 1.2.4 and 1.2.3........
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Ok I keep trying to attach or copy the fasta files in here but I keep getting an error.......
You can post the file at https://pastebin.com or via a GitHub
gist. People sometimes share files from google drive etc also.ok, added. thank you!
Are you using this web implementation: https://www.ebi.ac.uk/jdispatcher/msa/clustalo ? Are you using all the same options (click on
more optionslink to check all other option values) with your command line version.