diff --git a/algo/core/fasta.cpp b/algo/core/fasta.cpp
index 100c81110db336af446e670aeb633f8c7d7a22e8..49addc70e0329f515965723384fd979626a802ed 100644
--- a/algo/core/fasta.cpp
+++ b/algo/core/fasta.cpp
@@ -174,6 +174,7 @@ void OnlineFasta::init() {
   line_nb = 0;
   line = getInterestingLine();
   current.seq = NULL;
+  current_gaps = 0;
 }
 
 unsigned long long OnlineFasta::getPos() {
@@ -213,7 +214,18 @@ void OnlineFasta::skipToNthSequence() {
 
 void OnlineFasta::addLineToCurrentSequence(string line)
 {
-  current.sequence += line;
+  for (char& c : line)
+    {
+      if (c == ' ')
+        continue ;
+
+      if (c == '.') {
+        current_gaps++;
+        continue ;
+      }
+
+      current.sequence += c;
+    }
 }
 
 void OnlineFasta::next() {
@@ -227,6 +239,7 @@ void OnlineFasta::next() {
   if (current.seq) {
     delete [] current.seq;
     current.seq = NULL;
+    current_gaps = 0;
   }
 
   if  (hasNextData()) {
diff --git a/algo/core/fasta.h b/algo/core/fasta.h
index 7246507f37b36beffd7a1335f447753584fa40e1..c5c2f8648b716d4c5b4b8efed5486fd39a1b2f27 100644
--- a/algo/core/fasta.h
+++ b/algo/core/fasta.h
@@ -93,6 +93,8 @@ public:
 class OnlineFasta {
  private:
   Sequence current;
+  int current_gaps;
+
   istream *input;
   int extract_field;
   string extract_separator;