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