As a followup to my own post, you could make the loop more efficient by only using one regexp as follows:

while ( <INFILE> ) {
    chomp;
    if ( /^SEQRES[\s]{2,5}(1|2)\s/ ) {
       if ( $1 eq "1" ) {
            print "$_\n";
            print OUTFILE "$_\n";
       } else {
            last;
       }
    }
}
[download]

If I thought about it more I'm sure I could clean up that ugly cascading if statement too, but this works and is reasonably efficient.

Dave

"If I had my life to do over again, I'd be a plumber." -- Albert Einstein