Perhaps those questions illustrate the inadequacy of your specification.

Perhaps even more important, read about BioPerl, FASTA, and the vast array of other related options, many of which can be found using Google, site:CPAN, and appropriate search terms.

If you're still stuck after that, c'mon back with a more detailed question about some particular part of your project where you still have a problem. We're here to help you learn how to use Perl and its modules, but we need a manageable (and well specified) problem... and greatly prefer to see your efforts and help you overcome stumbling blocks than to simply hand you a solution.

Then use Perl's Pattern Matching feature to find each sequence of interest. By "tagging" do you mean insert a comment at that point where it was found? Use search-and-replace for that. Matching and replacing is a fundamental Perl primitive and one of the hallmarks of the language.

Write the results out.

BTW, I've heard of other people using Perl for DNA stuff, so look in CPAN and see if what you want is already there.

Solution in three easy steps:

• Uno: I think you are going to need to clearly describe what you mean by a sequence. For argument's sake I'll say you mean something like this, a sequence of capitalized letters (AGCTURYKMSWBDHVN) , one after another, followed by a single white space character (I borrowed this from here).
• Dos: You may run into some problems using Perl with extremely large files. Try reading up more about this so you can divide up your problem (either the files themselves, rewriting some things in C and using XS, etc.). A really simple example using the file format from the previous link is here:

  use strict;
  
  my $seqNum = 0;
  my %sequences = ();
  open(H,qq|$ARGV[0]|) or die $!;
  while(<H>)
  {
       while (m/\b([AGCTURYKMSWBDHVN]+)\b/g)
       {
            $sequences{++$seqNum} = $1;
       }
  }
  close(H);
  for (sort {$a <=> $b} keys %sequences){print qq|$_\t$sequences{$_}\n|}
  [download]

• Tres: Here is the kicker. Just because these letters satisfy the regex doesn't mean that they necessarily are valid sequences. You will need to compare them against a powerful sequence database like BLAST. There are modules to perform searches written in Perl, but you should first become acquainted with a suite of tools specifically built for these kinds of problems called Bioperl.

See also: Perl and Bioinformatics