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 matchADNG..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: ADNG..C.D
, ADNG..D.G
, 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 ~10e6-7
sequences).
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.
I am also aware of ScanProsite and Protein Pattern Find services. The first one is not error-prone, the second one is seems to be a web interface for grep
.
blastp
with input containing IUPAC ambiguous bases, and post-filter results to match your criteria? I'm uncertain how ambiguous bases are treated for proteins, as opposed to nucleotide searches, but that might be an avenue to explore. $\endgroup$