diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
index c20007cd6160e..4a99dfdd784ff 100644
--- a/sci-biology/tophat/tophat-2.0.8.ebuild
+++ b/sci-biology/tophat/tophat-2.0.8.ebuild
@@ -20,7 +20,7 @@ IUSE="debug"
 DEPEND="
 	dev-libs/boost
 	sci-biology/samtools
-	sci-biology/seqan"
+	~sci-biology/seqan-1.3.1"
 RDEPEND="${DEPEND}
 	sci-biology/bowtie"
 
diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
index 91cc2d4633301..d362ebe420020 100644
--- a/sci-biology/tophat/tophat-2.0.9.ebuild
+++ b/sci-biology/tophat/tophat-2.0.9.ebuild
@@ -21,7 +21,7 @@ IUSE="debug"
 DEPEND="
 	dev-libs/boost
 	sci-biology/samtools
-	sci-biology/seqan"
+	~sci-biology/seqan-1.3.1"
 RDEPEND="${DEPEND}
 	sci-biology/bowtie"