Open sanyalab opened 8 months ago
I recommend using the defaults. The options you mention are things that I've benchmarked in the past, in settling on the defaults, and that I don't prefer.
Thank you Sean. I had a follow-up question regarding MSA's.
Trimming and realignment (sometimes done manually) performed iteratively is supposed to improve the accuracy of HMM's. But how can one decide when to stop the trimming process? I am constantly debating this, as too much trimming will change the context of HMM and produce erroneous hits when I use these for searching protein DB's. Are there some metrics or tools to determine the maintenance of the general structure of MSA even after trimming?
Best Regards, Abhijit
Hello,
I have several protein MSA's and I was wondering about the parameters to use while building HMMs. I am aware of the default command, but was curious to know if there is an advantage or use-case on the different parameters. For example, is there a difference in the HMM's created when
--wgsc
is used as opposed to--wpb
. Or any use case of--plaplace
Thanks Abhijit