You don't really want to do it this way, of course... But I noticed that your data structure is very similar to Perl code, so...

use strict;
use warnings;

$_ = do { local $/; <> };

s/" "/" => "/g;
s/"\s{/" => {/g;
s/}/},/g;
s/;/,/g;

my $ds = eval "{$_}"; # Danger, Will Robinson!

my $new_sequence = "sequence.V6_0"; # or whatever.

for ( values %$ds )
{
    $_->{'StrCatDone'} eq '1' and
    $_->{'seq_name'} = $new_sequence;
}

use Data::Dumper;
# go as far as we can using Data::Dumper's output options...
$Data::Dumper::Indent = 0;
$Data::Dumper::Terse = 1;
$Data::Dumper::Pair = " ";

$_ = Dumper $ds;

# ...and do the rest by hand:
s/,/\n/g;
s/ {/\n{\n/g;
s/}/\n}/g;
s/'/"/g;
s/{(.*)}/$1/s;

print
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Execute the above with perl -i.bak.