diff --git a/conekt/controllers/specificity_comparison.py b/conekt/controllers/specificity_comparison.py
index 39d752b..7012386 100644
--- a/conekt/controllers/specificity_comparison.py
+++ b/conekt/controllers/specificity_comparison.py
@@ -72,6 +72,12 @@ def specificity_comparison_main():
             sequence_id_left = [r.profile.sequence_id for r in results_a if r.profile.sequence_id is not None]
             sequence_id_right = [r.profile.sequence_id for r in results_b if r.profile.sequence_id is not None]
 
+            abundance = defaultdict(lambda: False)
+
+            for r in results_a + results_b:
+                if r.profile.sequence_id is not None:
+                    abundance[r.profile.sequence_id] = r.profile.low_abundance
+
             interpro_id_to_name = {i.interpro_id: "%s (%s)" % (i.domain.label, i.domain.description if i.domain.description else "no description") for i in interpro_associations}
 
             for i in interpro_associations:
@@ -83,12 +89,14 @@ def specificity_comparison_main():
                 if i.sequence_id in sequence_id_left:
                     table_data[i.interpro_id]['left_genes'].append({'id': i.sequence_id,
                                                                     'name': i.sequence.name,
-                                                                    'shortest_alias': i.sequence.shortest_alias})
+                                                                    'shortest_alias': i.sequence.shortest_alias,
+                                                                    'low_abundance': abundance[i.sequence_id]})
 
                 if i.sequence_id in sequence_id_right:
                     table_data[i.interpro_id]['right_genes'].append({'id': i.sequence_id,
                                                                      'name': i.sequence.name,
-                                                                     'shortest_alias': i.sequence.shortest_alias})
+                                                                     'shortest_alias': i.sequence.shortest_alias,
+                                                                     'low_abundance': abundance[i.sequence_id]})
 
                 if len(table_data[i.interpro_id]['left_genes']) > 0 and len(table_data[i.interpro_id]['right_genes']) == 0:
                     table_data[i.interpro_id]['type'] = 'left'
@@ -124,7 +132,8 @@ def specificity_comparison_main():
 
                 table_data[f]['left_genes'].append({'id': r.profile.sequence_id,
                                                     'name': r.profile.sequence.name,
-                                                    'shortest_alias': r.profile.sequence.shortest_alias})
+                                                    'shortest_alias': r.profile.sequence.shortest_alias,
+                                                    'low_abundance': r.profile.low_abundance})
 
             for r in results_b:
                 f = seq_to_fam[r.profile.sequence_id] if r.profile.sequence_id in seq_to_fam.keys() else None
@@ -137,7 +146,9 @@ def specificity_comparison_main():
 
                 table_data[f]['right_genes'].append({'id': r.profile.sequence_id,
                                                      'name': r.profile.sequence.name,
-                                                     'shortest_alias': r.profile.sequence.shortest_alias})
+                                                     'shortest_alias': r.profile.sequence.shortest_alias,
+                                                     'low_abundance': r.profile.low_abundance
+                                                     })
 
             for f in table_data.keys():
                 if len(table_data[f]['left_genes']) > 0 and len(table_data[f]['right_genes']) == 0:
diff --git a/conekt/templates/compare_specificity.html b/conekt/templates/compare_specificity.html
index 84442d0..0e9ce67 100644
--- a/conekt/templates/compare_specificity.html
+++ b/conekt/templates/compare_specificity.html
@@ -130,7 +130,8 @@ <h2 class="text-muted"><em>{{ labels.left_species }}</em> {{ labels.left_conditi
                                             {% for l in td.left_genes %}
                                                 <a href="{{ url_for('sequence.sequence_view', sequence_id=l.id) }}"
                                                 class="qtip_tooltip"
-                                                qtip_href="{{ url_for('sequence.sequence_tooltip', sequence_id=l.id) }}">{{l.name}}</a>{%- if l.shortest_alias %} <span class="text-muted">({{ l.shortest_alias }})</span>{%- endif -%}{%- if not loop.last -%}, {%- endif -%}
+                                                qtip_href="{{ url_for('sequence.sequence_tooltip', sequence_id=l.id) }}">{{l.name}}</a>{%- if l.low_abundance %} <span class="warning-message qtip_tooltip"
+                               qtip_href="{{ url_for('help.help_popup', topic='lowabundance') }}"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i></span>{%- endif -%}{%- if l.shortest_alias %} <span class="text-muted">({{ l.shortest_alias }})</span>{%- endif -%}{%- if not loop.last -%}, {%- endif -%}
                                             {% else %}
                                                 <span class="text-muted text-center">-</span>
                                             {% endfor %}
@@ -139,7 +140,8 @@ <h2 class="text-muted"><em>{{ labels.left_species }}</em> {{ labels.left_conditi
                                             {% for r in td.right_genes %}
                                                 <a href="{{ url_for('sequence.sequence_view', sequence_id=r.id) }}"
                                                 class="qtip_tooltip"
-                                                qtip_href="{{ url_for('sequence.sequence_tooltip', sequence_id=r.id) }}">{{r.name}}</a>{%- if r.shortest_alias %} <span class="text-muted">({{ r.shortest_alias }})</span>{%- endif -%}{%- if not loop.last -%}, {%- endif -%}
+                                                qtip_href="{{ url_for('sequence.sequence_tooltip', sequence_id=r.id) }}">{{r.name}}</a>{%- if r.low_abundance %} <span class="warning-message qtip_tooltip"
+                               qtip_href="{{ url_for('help.help_popup', topic='lowabundance') }}"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i></span>{%- endif -%}{%- if r.shortest_alias %} <span class="text-muted">({{ r.shortest_alias }})</span>{%- endif -%}{%- if not loop.last -%}, {%- endif -%}
                                             {% else %}
                                                 <span class="text-muted  text-center">-</span>
                                             {% endfor %}