I am running blastx on a standalone version of blast-2.2.31+. Using the standard genetic code each stop codon (TAA, TAG, TGA) is represented by the asterisk symbol '*'.
Is it possible to amend the genetic code to give each stop codon an individual symbol? for example TAA '£', TAG '$', TGA '%'
When I try to amend Genetic_code_table.cpp and Genetic_code.hpp I get the following errors.
Error: (803.7) [blastx] Genetic-code-table.E.E.ncbieaa
Bad char [0xC2] in string at line 3
FFLLSSSSYY£$CC%WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Error: (803.7) [blastx] Genetic-code-table.E.E.ncbieaa
Bad char [0xA3] in string at line 3
FFLLSSSSYY£$CC%WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Error: basic_string::substr
I am not an expert in C++ any help would be great!
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There's nothing stopping you, although I don't know if you'd want to try it if you weren't familiar with C++.
If I may ask, what is the motivation for doing this? Don't forget that BLASTX is scanning multiple reading frames, so including a symbol like that would be difficult.
I'm looking into stop codon reassignment and the standard genetic code (and the other codes) don't distinguish between them, they are all '*'. The source code is written in C++ and I take it can only be amended in said language, or am I mistaken? I haven't looked at source codes before.