diff --git a/src/main/java/org/cqfn/astranaut/core/algorithms/SubtreeBuilder.java b/src/main/java/org/cqfn/astranaut/core/algorithms/SubtreeBuilder.java
index 46cefe9..cbb2445 100644
--- a/src/main/java/org/cqfn/astranaut/core/algorithms/SubtreeBuilder.java
+++ b/src/main/java/org/cqfn/astranaut/core/algorithms/SubtreeBuilder.java
@@ -43,13 +43,14 @@ public class SubtreeBuilder {
     /**
      * Algorithm that composes a subtree only from the nodes that are specified in the set.
      */
-    public static final Algorithm INCLUDE = (node, set) -> set.contains(node);
+    public static final Algorithm INCLUDE = SubtreeBuilder::isPresentInSet;
 
     /**
      * Algorithm that composes a subtree from all nodes in the original tree,
      *  but excludes nodes specified in the set.
      */
-    public static final Algorithm EXCLUDE = (node, set) -> !set.contains(node);
+    public static final Algorithm EXCLUDE =
+        (node, set) -> !SubtreeBuilder.isPresentInSet(node, set);
 
     /**
      * The root node of the original tree.
@@ -118,6 +119,20 @@ private void build(final Node node, final Map<Node, List<Integer>> indexes,
         }
     }
 
+    /**
+     * Checks whether a node or its prototype is present in the node set.
+     * @param node Node to be checked
+     * @param set Set of nodes
+     * @return Checking result.
+     */
+    private static boolean isPresentInSet(final Node node, final Set<Node> set) {
+        boolean result = set.contains(node);
+        if (!result && node instanceof PrototypeBasedNode) {
+            result = SubtreeBuilder.isPresentInSet(((PrototypeBasedNode) node).getPrototype(), set);
+        }
+        return result;
+    }
+
     /**
      * An algorithm that selects nodes based on some criteria.
      * @since 1.1.4
diff --git a/src/main/java/org/cqfn/astranaut/core/base/PatternNode.java b/src/main/java/org/cqfn/astranaut/core/base/PatternNode.java
index 95718d1..d17701f 100644
--- a/src/main/java/org/cqfn/astranaut/core/base/PatternNode.java
+++ b/src/main/java/org/cqfn/astranaut/core/base/PatternNode.java
@@ -125,14 +125,11 @@ private static List<PatternItem> initChildrenList(final Node original) {
         final List<PatternItem> result = new ArrayList<>(count);
         for (int index = 0; index < count; index = index + 1) {
             final Node child = original.getChild(index);
-            if (child instanceof DiffNode) {
-                result.add(
-                    new PatternNode(((DiffNode) child).getPrototype())
-                );
-            } else if (child instanceof Action) {
-                result.add((PatternItem) child);
-            } else {
+            final Action action = Action.toAction(child);
+            if (action == null) {
                 result.add(new PatternNode(child));
+            } else {
+                result.add(action);
             }
         }
         return result;
diff --git a/src/test/java/org/cqfn/astranaut/core/algorithms/PatternBuilderTest.java b/src/test/java/org/cqfn/astranaut/core/algorithms/PatternBuilderTest.java
index 51ab716..457a71e 100644
--- a/src/test/java/org/cqfn/astranaut/core/algorithms/PatternBuilderTest.java
+++ b/src/test/java/org/cqfn/astranaut/core/algorithms/PatternBuilderTest.java
@@ -35,6 +35,7 @@
 import org.cqfn.astranaut.core.base.Hole;
 import org.cqfn.astranaut.core.base.Node;
 import org.cqfn.astranaut.core.base.Pattern;
+import org.cqfn.astranaut.core.base.Replace;
 import org.cqfn.astranaut.core.base.Tree;
 import org.cqfn.astranaut.core.example.green.Addition;
 import org.cqfn.astranaut.core.example.green.ExpressionStatement;
@@ -89,9 +90,9 @@ void creatingPatternFromSubtree() {
         final Node var = ctor.createNode();
         ctor = new IntegerLiteral.Constructor();
         ctor.setData("1");
-        final Node second = ctor.createNode();
+        final Node before = ctor.createNode();
         ctor = new Addition.Constructor();
-        ctor.setChildrenList(Arrays.asList(var, second));
+        ctor.setChildrenList(Arrays.asList(var, before));
         final Node addition = ctor.createNode();
         ctor = new Variable.Constructor();
         ctor.setData("x");
@@ -108,19 +109,23 @@ void creatingPatternFromSubtree() {
         ctor.setChildrenList(Arrays.asList(stmt, ret));
         final Node block = ctor.createNode();
         final Tree tree = new Tree(block);
+        ctor = new IntegerLiteral.Constructor();
+        ctor.setData("2");
+        final Node after = ctor.createNode();
+        final DiffTreeBuilder diffbuilder = new DiffTreeBuilder(tree);
+        diffbuilder.replaceNode(before, after);
+        final DiffTree diff = diffbuilder.getDiffTree();
         final Set<Node> exclude = new HashSet<>();
         exclude.add(ret);
         final Tree subtree = new Tree(
-            new SubtreeBuilder(tree, SubtreeBuilder.EXCLUDE).create(exclude)
+            new SubtreeBuilder(diff, SubtreeBuilder.EXCLUDE).create(exclude)
         );
-        final PatternBuilder builder = new PatternBuilder(subtree);
-        builder.makeHole(var, 1);
-        final Pattern pattern = builder.getPattern();
-        Assertions.assertNotNull(pattern);
+        final PatternBuilder ptbuilder = new PatternBuilder(subtree);
+        ptbuilder.makeHole(var, 1);
+        final Pattern pattern = ptbuilder.getPattern();
         final DepthFirstWalker traversal = new DepthFirstWalker(pattern.getRoot());
-        final Optional<Node> hole = traversal.findFirst(node -> node instanceof Hole);
-        Assertions.assertTrue(hole.isPresent());
-        Assertions.assertEquals("#1",  hole.get().getData());
+        Assertions.assertTrue(traversal.findFirst(node -> node instanceof Replace).isPresent());
+        Assertions.assertTrue(traversal.findFirst(node -> node instanceof Hole).isPresent());
     }
 
     @Test