Note: this question was also asked on biostars
are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files?
For example, I want to know, which proteins in my fasta file to match
ADNG..C.G regexp (which represents
ADNGCG pattern). However, I want to be tolerant to matching errors, meaning that I'm good with any protein that differs in any 1 letter in the motif:
MDNG..C.G, etc are all good. Running all possible variants through
grep is possible, but exponentially long for longer patterns (I usually have
15-20 letters in pattern, and scan
I am aware of the tool
agrep (docs. As far as I know, it's not supported anymore, and also does not distinguish letters in which it's allowed to make error. Also, it does not support long enough patterns (with more than 9 errors -- and yes, I tried to recompile it with myself from here and could not get it work). Also, it's not designed for proteins specifically.