Hello,

I'm just writing a script that will perform a number of different, very simple regular expressions on a large (up to 300 million characters) string. The searches are really simple, things like:

while ( $sequence =~ /CACGTG/g ) {
        print join("\t", $chr, '+', pos($sequence)-6), "\n";
        }

while ( $sequence =~ /GTGCAC/g ) {
        print join("\t", $chr, '-', pos($sequence)-6), "\n";
        }

[download]

I have two questions about this. First, am I right to be doing these searches sequentially? Or ought I be trying to combine them all into one single regular expression? I chose the sequential approach because it seemed far more readable and easily scalable, but I didn't know if there was any reason to believe it was horribly inefficient or silly.

Second, is my use of pos($sequence) - match_length to find the starting point of the match appropriate, or is there a simpler way of getting the match start?

Many thanks in advance for any thoughts/advice/comments.

In reply to Multiple Regex's on a Big Sequence by bernanke01

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