diff --git a/src/main/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParser.java b/src/main/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParser.java
index 2a1ce4b..ffeca6c 100644
--- a/src/main/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParser.java
+++ b/src/main/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParser.java
@@ -13,10 +13,15 @@
 import pl.poznan.put.structure.formats.DefaultDotBracket;
 import pl.poznan.put.structure.formats.DotBracket;
 
+import java.util.Arrays;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+
 @Component
 public class SecondaryFileParser {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(SecondaryFileParser.class);
+    private static final Pattern WHITESPACE_PATTERN = Pattern.compile("\\s+");
     private final Converter converter;
 
     public DotBracket parseSecondaryFile(String content, InputType inputType, boolean removeIsolated) {
@@ -38,9 +43,10 @@ public DotBracket parseSecondaryFile(String content, InputType inputType, boolea
 
     private DotBracket convertBpSeqIntoDotBracket(String content, boolean removeIsolated) {
         try {
+            String normalizedContent = normalizeSecondaryFileContent(content);
             BpSeq bpSeq = removeIsolated
-                    ? BpSeq.fromString(content).withoutIsolatedPairs()
-                    : BpSeq.fromString(content);
+                    ? BpSeq.fromString(normalizedContent).withoutIsolatedPairs()
+                    : BpSeq.fromString(normalizedContent);
             Ct ct = Ct.fromBpSeq(bpSeq);
             return DefaultDotBracket.copyWithStrands(converter.convert(bpSeq), ct);
         } catch (IllegalArgumentException exception) {
@@ -52,9 +58,10 @@ private DotBracket convertBpSeqIntoDotBracket(String content, boolean removeIsol
 
     private DotBracket convertCtIntoDotBracket(String content, boolean removeIsolated) {
         try {
+            String normalizedContent = normalizeSecondaryFileContent(content);
             Ct ct = removeIsolated
-                    ? Ct.fromString(content).withoutIsolatedPairs()
-                    : Ct.fromString(content);
+                    ? Ct.fromString(normalizedContent).withoutIsolatedPairs()
+                    : Ct.fromString(normalizedContent);
             BpSeq bpSeq = BpSeq.fromCt(ct);
             return DefaultDotBracket.copyWithStrands(converter.convert(bpSeq), ct);
         } catch (IllegalArgumentException exception) {
@@ -79,6 +86,14 @@ private DotBracket readDotBracketContent(String content, boolean removeIsolated)
         }
     }
 
+    private String normalizeSecondaryFileContent(String content) {
+        return Arrays.stream(content.split("\\R"))
+                .map(String::trim)
+                .filter(line -> !line.isEmpty())
+                .map(line -> WHITESPACE_PATTERN.matcher(line).replaceAll(" "))
+                .collect(Collectors.joining("\n"));
+    }
+
     @Autowired
     public SecondaryFileParser(Converter converter) {
         this.converter = converter;
diff --git a/src/test/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParserTest.java b/src/test/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParserTest.java
new file mode 100644
index 0000000..045afff
--- /dev/null
+++ b/src/test/java/pl/poznan/put/rnapdbee/engine/shared/parser/SecondaryFileParserTest.java
@@ -0,0 +1,56 @@
+package pl.poznan.put.rnapdbee.engine.shared.parser;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import pl.poznan.put.rnapdbee.engine.shared.domain.InputType;
+import pl.poznan.put.structure.formats.BpSeq;
+import pl.poznan.put.structure.formats.Converter;
+import pl.poznan.put.structure.formats.DefaultDotBracket;
+import pl.poznan.put.structure.formats.DotBracket;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class SecondaryFileParserTest {
+
+    @Mock
+    private Converter converter;
+
+    @InjectMocks
+    private SecondaryFileParser secondaryFileParser;
+
+    @Test
+    void shouldParseBpSeqWithRedundantSpacesAndEmptyLines() {
+        String content = "1 A 4\n2   U 3\n\n 3 G  2\n4 C   1\n";
+        DotBracket conversionResult = mock(DotBracket.class);
+        when(conversionResult.sequence()).thenReturn("AAAA");
+        when(conversionResult.structure()).thenReturn("()()");
+        when(converter.convert(any(BpSeq.class))).thenReturn(conversionResult);
+
+        DotBracket result = secondaryFileParser.parseSecondaryFile(content, InputType.BPSEQ, false);
+
+        assertThat(result).isNotNull();
+        verify(converter).convert(any(BpSeq.class));
+    }
+
+    @Test
+    void shouldParseCtWithRedundantSpacesAndEmptyLines() {
+        String content = " 4   some header\n1 A 0 2 4 1\n 2 U 1 3 3 2\n\n3 G 2 4 2 3\n4 C 3 0 1 4\n";
+        DotBracket conversionResult = mock(DotBracket.class);
+        when(conversionResult.sequence()).thenReturn("AAAA");
+        when(conversionResult.structure()).thenReturn("()()");
+        when(converter.convert(any(BpSeq.class))).thenReturn(conversionResult);
+
+        DotBracket result = secondaryFileParser.parseSecondaryFile(content, InputType.CT, false);
+
+        assertThat(result).isNotNull();
+        verify(converter).convert(any(BpSeq.class));
+    }
+}