diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in
--- EMBOSS-6.3.1/configure.in.system-expat	2010-11-09 15:05:50.600682002 -0500
+++ EMBOSS-6.3.1/configure.in	2010-11-09 15:06:25.101681999 -0500
@@ -424,6 +424,7 @@ AC_ARG_ENABLE(systemlibs,
 if test "${enable_systemlibs}" = "yes" ; then
     have_systemlibs=yes
     AC_CHECK_LIB(pcre, pcre_compile)
+    AC_CHECK_LIB(expat, XML_ParserCreate)
 fi          
 AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
 AC_SUBST(ESYSTEMLIBS)
@@ -660,7 +661,7 @@ CHECK_THREADS
 
 
 AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
-ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
+ajax/zlib/Makefile ajax/core/Makefile
 ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
 ajax/acd/Makefile
 emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile
diff -up EMBOSS-6.3.1/configure.system-expat EMBOSS-6.3.1/configure
--- EMBOSS-6.3.1/configure.system-expat	2010-11-09 15:05:50.603682002 -0500
+++ EMBOSS-6.3.1/configure	2010-11-09 15:06:59.620682003 -0500
@@ -14946,6 +14946,51 @@ _ACEOF
 
 fi
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for XML_ParserCreate in -lexpat" >&5
+$as_echo_n "checking for XML_ParserCreate in -lexpat... " >&6; }
+if test "${ac_cv_lib_expat_XML_ParserCreate+set}" = set; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lexpat  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char XML_ParserCreate ();
+int
+main ()
+{
+return XML_ParserCreate ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_expat_XML_ParserCreate=yes
+else
+  ac_cv_lib_expat_XML_ParserCreate=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_expat_XML_ParserCreate" >&5
+$as_echo "$ac_cv_lib_expat_XML_ParserCreate" >&6; }
+if test "x$ac_cv_lib_expat_XML_ParserCreate" = x""yes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBEXPAT 1
+_ACEOF
+
+  LIBS="-lexpat $LIBS"
+
+fi
+
 fi
  if test "$have_systemlibs" = "yes"; then
   ESYSTEMLIBS_TRUE=
@@ -15299,7 +15344,7 @@ fi
 
 
 
-ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
+ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -16357,7 +16402,6 @@ do
     "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;;
     "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;;
     "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;;
-    "ajax/expat/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/expat/Makefile" ;;
     "ajax/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/zlib/Makefile" ;;
     "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;;
     "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;;