Scoring Matrix and NWalign

Hey all,

I'm trying to use the NWalign algorithm in MATLAB, but my application is different than the standard usage. As such, I need to specify a custom scoring matrix. MATLAB's help files suggest that custom scoring matrices can be used, however the help files don't provide examples on how to specify the input parameters to accept this matrix. Would anyone be able to provide any suggestions on this issue?

Thank you all.

Bill

[mariam issa]

I am having the same problem right now