It might be helpful if you told us what patterns you were looking for using English, because your regexes seem a bit strange.

As for solving your basic problem (print until X line, then stop until Y line, then start again), you might consider a state machine; that is, use a global variable that keeps track of whether you're printing or not, and change it inside the loop if the conditions change--and then just print at the end of the loop when the variable tells you you're supposed to be printing.

Hi ssandv
I want to remove the text starting at "COMMENT" and just before the line that starts with FEATURES.
Read more... (5 kB)

Then print from "FEATURES" until the end of the line.
LomSpace

So it appears that sections of the file are defined by words in all caps starting in column 0. This actually lends itself pretty well to keeping track of the state (in this case the file section) you're in.

There are many other ways to do it, but this is an example of what I was suggesting:

my $state;

while (my $line=<$in>) {
    if ($line=~/^([A-Z]+)/) {
        $state=$1;
    }
    print $line unless $state eq "COMMENT";
}
[download]

which outputs:

07:37<sandvik@sat1> ~/perl$ ./pmtest.pl
LOCUS       4                     302276 bp    DNA     linear   HTG 31
+-OCT-2008
DEFINITION  Mus musculus chromosome 4 NCBIM37 partial sequence
            138489260..138791535 reannotated via EnsEMBL
ACCESSION   chromosome:NCBIM37:4:138489260:138791535:-1
KEYWORDS    .
SOURCE      house mouse.
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Eutele
+ostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
            Sciurognathi; Muroidea; Muridae; Murinae; Mus.
FEATURES             Location/Qualifiers
     source          1..302276
                     /db_xref="taxon:10090"
                     /organism="Mus musculus"
     gene            complement(267261..268504)
                     /note="locus_tag=Rnf186"
                     /gene="ENSMUSG00000070661"
                     /note="ring finger protein 186 [Source:MGI;Acc:MG
+I:1914075]
[download]

Hi toolic!
This is a dynamic situation, so range operators won't do.
I want to remove the text starting at "COMMENT" and
just before the line that starts with FEATURES.
Read more... (5 kB)

Then print from "FEATURES" until the end of the line.
LomSpace

Perhaps I do not understand your requirements. It would help if you were to also post your desired output. Here is an example using range operators:
Read more... (5 kB)

This is the output:

Read more... (1352 Bytes)

1st : next what ? on line 6 of your code sample: You are not in a loop.

To skip a block of lines, between 2 regexes, skipping the lines with the regexes too, I should write :

 
my $inBlock = 0;
while(<$in>) 
{
  if ($inBlock) 
  {
    $inBlock = 0 if ( $_ =~ /2nd Regex/);
  }
  else
  { 
    $inBlock = 1 if ( $_ =~ /1st Regex/);
    print $_ if(!$inBlock);
  }
}
[download]

ssandv gave you a good pointer. because from the code that you presented you are looping through a whole file and printing stuff, then exiting the loop keeping the file handle opened (which i strongly disapprove), then trying to capture something from the filehandle and then again repeating the first step.you gotta admit you intentions are a bit confusing ;) maybe something like this will help:

use strict;


...
my $trigger = 0;

while(<$in>){
    print $out $_ if ($trigger == 0);
    $trigger = 1 if ($_=~/match something|or something else/g);
    $trigger = 0 if ($_=~/match something|or something else/g);
}
[download]

cheers