Using BLASTp with Custom Substitution Matrices

Question

[H.Hasani]

Hi all,

was wondering if anyone has tried to use recent BLASTp with custom substitution matrices instead of the predefined ones (PAMs & BLOSUMs)? It has been discussed about 12 years ago (see this post) but clearly the suggested solutions are outdated as they address the releases at the time which were build with c-toolkit while the current releases (e.g. > 2.14.0) are c++ toolkit based. NCBI kindly replied that the matrices are built into the binary and therefore it might not be possible to take this rout anymore. I still need to be 100% sure that is approach is entirely impossible at this point.

Any suggestion or help are highly appreciated.

Thanks

Answer 1

[biofalconch]

I'm no expert on this but maybe have a look how rmblast does it:

https://www.repeatmasker.org/rmblast/

Best of luck!