I'm assuming $line7 contains the excessive amount of data that you've posted. In the script below, I've used a representative sample. For future posts, please do the same.

You haven't shown how you've extracted that data. Ensure $line7 actually contains the data you think it does (i.e. print "$line7\n";).

In the script below, I've simply captured everything that isn't a double-quote between '/translation="' and '"' then removed all the extraneous whitespace. 

#!/usr/bin/env perl -l

use strict;
use warnings;

my $line7 = '
...
                     /db_xref="GI:2735715"
                     /translation="MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPA
+GDRGPRGER
                     GPPGPPGRDGEDGPTGPPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPM
+GLMGPRGPP

                     YASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYT
+VLVDGCSKK
                     TNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK"
     exon            2432..2501
...
';

my $re = qr{/translation="([^"]+)"};

my ($extract) = $line7 =~ $re;

$extract =~ s/\s+//g;

print $extract;

[download]

Output:

MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGP
+PGLGGNFAAQYDGKGVGLGPGPMGLMGPRGPPYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVE
+LVAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK

[download]

Update: From looking at other posts in this thread, it would seem possible that your initial problem (i.e. before you even start performing any matching) could be extracting the data you want. If that's the case, open a filehandle to your data file and populate $line7 as I've shown below. As you'll see, once you've done that, the rest of the code hasn't changed and the output is identical.

By the way, is there some significance to the $line7 variable name? If not, I'd pick something more meaningful. 

#!/usr/bin/env perl -l

use strict;
use warnings;

my $line7 = '';

my $re = qr{/translation="([^"]+)"};

while (<DATA>) {
    if (/^\s+\/translation=/ .. /^\s+exon/) {
        $line7 .= $_;
    }
    else {
        $line7 ? last : next;
    }
} 

my ($extract) = $line7 =~ $re;

$extract =~ s/\s+//g;

print $extract;

__DATA__
...
                     /db_xref="GI:2735715"
                     /translation="MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPA
+GDRGPRGER
                     GPPGPPGRDGEDGPTGPPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPM
+GLMGPRGPP

                     YASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYT
+VLVDGCSKK
                     TNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK"
     exon            2432..2501
...

[download]

Output:

MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGP
+PGLGGNFAAQYDGKGVGLGPGPMGLMGPRGPPYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVE
+LVAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK

[download]

-- Ken

In reply to Re: Help to build a REGEXP by kcott
in thread Help to build a REGEXP by Anonymous Monk

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