Use lc to lower case the words used as keys for the lookup hash and lower case the search text. The code already finds long protein names which have a prefix that is the same as a shorter protein's name. I've added a splice to avoid finding a short protein that matches a part of the long protein name that has just been found. Oh, and I updated the print to generate the desired output.

use strict;
use warnings;

my $sentence = 'a long mixed case name protein is found in preference 
+to a mixed case name protein which is found before a short protein';

my %proteinLU;

while (<DATA>) {
    chomp;

    my $protein = $_;
    my @parts = split;
    my $parent = \%proteinLU;

    while (@parts) {
        my $part = lc shift @parts;

        $parent = $parent->{$part} ||= {};
        next if @parts;
        $parent->{_name_} = $protein;
    }
}

my @words = map {lc} split ' ', $sentence;

while (@words) {
    my $word = shift @words;

    if (! exists $proteinLU{$word}) {
        print "$word ";
        next;
    }

    my $parent = $proteinLU{$word};
    my $wIndex = 0;

    while ($wIndex < @words && exists $parent->{$words[$wIndex]}) {
        $parent = $parent->{$words[$wIndex++]}
    }

    print "**$parent->{_name_}** " if exists $parent->{_name_};
    splice @words, 0, $wIndex;
}


__DATA__
long Mixed Case name protein
Mixed Case name protein
Protein

[download]

Prints:

a **long Mixed Case name protein** is found in preference to a **Mixed
+ Case name protein** which is found before a short **Protein**

[download]
True laziness is hard work

In reply to Re^4: Tag protein names in sentences by GrandFather
in thread Tag protein names in sentences by sinlam

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