You don't show us the relevant code or a Short Self-Contained Code Example, so I can only guess.

Most likely you are doing a simple substring match instead of looking for word boundaries. See perlre on word boundaries, \b.

my $protein = 'NOV';
my @keywords = (qw(novice niveau november paramonov nov supernova), "h
+e said 'nov'");
print "Left-matches  /$protein/: $_\n" for grep { $_ =~ /\b$protein/i 
+} @keywords;
print "Right-matches /$protein/: $_\n" for grep { $_ =~ /$protein\b/i 
+} @keywords;
print "Contains      /$protein/: $_\n" for grep { $_ =~ /$protein/i } 
+@keywords;
print "Contains      /$protein/ as word: $_\n" for grep { $_ =~ /\b$pr
+otein\b/i } @keywords;
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