Your html still has some problems, but some are easily fixed by simply revising the quoting. Some may frown, and with reason, at this use of a 'heredoc' but it "just works" for a one-off:

#!/usr/bin/perl
use 5.012;

my $protein = "chuck steak";

my $heredoc = <<END

<table border="1" width="50%" bgcolor="#CCFFFF">
<tr><td><b>  Peptide sequence frame 1</b></td></tr>\n
<tr><td>$protein </td> <td>also 'walnuts'</td></tr>
</table>
END
;

print $heredoc;
[download]

OUTPUT:

<table border="1" width="50%" bgcolor="#CCFFFF">
<tr><td><b>  Peptide sequence frame 1</b></td></tr>

<tr><td>chuck steak </td> <td>also 'walnuts'</td></tr>
</table>
[download]

Note the newline at the end of line 09; your empty tr></tr> will provoke complaints from some validators.

Better, however, to devote a couple hours to familiarizing yourself with CSS1 and 2. And better yet to follow the broad guidance provided by blue_cowdawg ( above ) and to use such CSS constructs as "max-width: nn%" to assure that the wraps work (...err, semi-work.....) based on the user's current screen width.