I'm especially interested in how sequence searching and matching work in libraries like this. Seq has a "match" statement for this task, which implements ACGT c

I'm especially interested in how sequence searching and matching work in libraries like this. Seq has a "match" statement for this task, which implements ACGT characters and _ for a single wildcard base and "..." for multiple wildcard bases, and a recursive matching system I haven't quite grokked yet. Personally I'm more comfortable with a regular expression syntax, so would prefer "." and ".*". Actually, even better than "." is "N" from the IUPAC notation: https://en.wikipedia.org/wiki/Nucleic_acid_notation https://en.wikipedia.org/wiki/Nucleic_acid_notation The IUPAC notation is nice because it standardises "character classes" for working with nucleic acid sequences. For example, "B" is "[CGT]". I wrote a module a while ago for searching nucleic acid sequences with regexps: https://metacpan.org/pod/Bio::Regexp https://metacpan.org/pod/Bio::Regexp When working with sequences there are a bunch of things to think about that aren't really obvious from other types of data (or at least weren't obvious to me!) Exhaustive search: Often a regexp can match in many ways, and most regexp systems don't provide a way to get a complete list of them all. Fortunately there is the Regexp::Exhaustive perl module which is what I used. The way this module works is pretty awesome. It adds a special "FAIL" directive to the end of a pattern, so that the match can be recorded and artificially failed, triggering the regexp engine's backtracking mechanism to back up and find the next match (if any). Reverse complements: Because DNA is double-stranded (well, usually... this is biology after all) there is a "complementary" pattern on the first strand that corresponds to the pattern you are interested in on the other strand. You almost always need to search for both. And what's more, DNA is directional so you actually need to search in the reverse direction for this complementary pattern. You can either reverse and complement your sequence (which seq has a special ~ operator for, neat!) and search again, or reverse and complement the search pattern itself, assemble a single combined regexp (Regexp::Assemble module), and do a single scan over the data, which is what Bio::Regexp does. Circular DNA: Some DNA (plasmids) are actually circular in shape, meaning the start is connected to the end. So a comprehensive search needs to check for cases where the desired patterns span the arbitrary location selected as the "start" in your sequence.