Okay you changed the question a few times while I was composing this reply ;o). Have to say i'm still left guessing what the ordering rules are for the angle bracket segments. I picked one ordering that gives the results you're requesting, but you may still have to tweak them a bit. The main idea is to ignore whitespace in the regex using the /x parameter so that you can format the regex for readability:

use strict;
use warnings;

while (<DATA>) {
        print if /
          <MIR-\d+>
          (     <EXP-V-\d+>
                (<ART-\d+>)*
                (<BE-V>)*
             |  <ASSC-PHRASE-\d+>
          )
          <VACCVIRUS-PROP-\d+>/x;
}

__DATA__
<MIR-1><EXP-V-3><VACCVIRUS-PROP-1>
<MIR-1><ASSC-PHRASE-1><VACCVIRUS-PROP-1><PATTERN-1>
<MIR-1><EXP-V-0><ART-0><VACCVIRUS-PROP-1>
<MIR-1><EXP-V-0><ART-0><BE-V><VACCVIRUS-PROP-1>
<MIR-1><EXP-V-0><EXP-N-0><VACCVIRUS-PROP-1>

[download]

In reply to Re: Combining Regex by Loops
in thread Combining Regex by neversaint

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.