Hello everyone,
I'm trying to perform a MSA of 130 protein sequences with a mean size of ~146 aa. I'm using the functions of the ips package to run MAFFT, Clustal, MUSCLE, T-Coffe etc. in R as external applications.
I was able to perform MSA using coding sequences for the same proteins. But when I translated the coding sequences and ran the different MAFFT models, the final alignment was missing many sites and the average final size of the sequences was only ~ 104 aa. Somehow, many residues are gone. This problem did not occur with the other alignment software such as Clustal, MUSCLE and T-Coffee. Also, when I ran the same data set on the MAFFT web server, the MSA was correct. So I imagine it must be a problem with my script, or maybe with the 'mafft' function in the ips package.
- I read the coding sequences with
xdna
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