diff -up EMBOSS-6.6.0/configure.in.system-expat EMBOSS-6.6.0/configure.in
--- EMBOSS-6.6.0/configure.in.system-expat	2015-10-30 09:30:20.978720930 -0400
+++ EMBOSS-6.6.0/configure.in	2015-10-30 09:31:33.117227536 -0400
@@ -810,6 +810,7 @@ AC_ARG_ENABLE([systemlibs],
 [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
 if test "x${enable_systemlibs}" = "xyes" ; then
    AC_CHECK_LIB(pcre, pcre_compile)
+   AC_CHECK_LIB(expat, XML_ParserCreate)
 fi
 AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
 
@@ -962,7 +963,6 @@ AC_CONFIG_FILES([Makefile
                  ajax/ajaxdb/Makefile
                  ajax/core/Makefile
                  ajax/ensembl/Makefile
-                 ajax/expat/Makefile
                  ajax/graphics/Makefile
                  ajax/zlib/Makefile
                  doc/Makefile