diff -up EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/acd/Makefile.am
--- EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre	2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/acd/Makefile.am	2011-11-23 17:03:07.033953627 +0100
@@ -13,11 +13,11 @@ CYGWIN_LDACD = -L../../plplot -L../pcre
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 endif
 
 AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+-I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/graphics \
 -I$(top_srcdir)/ajax/ensembl \
diff -up EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre	2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am	2011-11-23 17:03:07.033953627 +0100
@@ -13,13 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pc
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 endif
 
 
 AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/plplot \
--I$(top_srcdir)/ajax/pcre \
 $(EXTRA_INCLUDES) \
 $(AXIS2C_CPPFLAGS) \
 -I$(top_srcdir)/ajax/ensembl
diff -up EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.4.0/ajax/core/ajreg.h
--- EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre	2010-04-14 09:44:20.000000000 +0200
+++ EMBOSS-6.4.0/ajax/core/ajreg.h	2011-11-23 17:03:07.034953633 +0100
@@ -16,9 +16,8 @@ extern "C"
 #define ajreg_h
 
 #include "ajax.h"
-#include "pcre_config.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
 
 #define AJREG_OVECSIZE 30
 
@@ -41,7 +40,7 @@ extern "C"
 ******************************************************************************/
 
 typedef struct AjSRegexp {
-    real_pcre *pcre;
+    struct real_pcre *pcre;
     pcre_extra *extra;
     int *ovector;
     const char* orig;
diff -up EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/core/Makefile.am
--- EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre	2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/core/Makefile.am	2011-11-23 17:03:07.035953639 +0100
@@ -12,14 +12,14 @@ CYGWIN_LDAJAX = -L../../plplot -L../expa
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 endif
 
 
 AM_CPPFLAGS = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
 -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
 $(MYSQL_CPPFLAGS) $(POSTGRESQL_CPPFLAGS) \
--I. -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+-I. -I$(top_srcdir)/plplot $(EXTRA_INCLUDES)
 
 AJAXSRC = ajalign.c ajarr.c \
 ajassem.c ajassemread.c ajassemwrite.c \
diff -up EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ensembl/Makefile.am
--- EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre	2011-07-07 00:01:27.000000000 +0200
+++ EMBOSS-6.4.0/ajax/ensembl/Makefile.am	2011-11-23 17:03:07.035953639 +0100
@@ -10,14 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../e
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
 endif
 
 
 AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/plplot \
-$(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre
+$(EXTRA_INCLUDES)
 
 ENSEMBLSRC = \
 ensalign.c \
diff -up EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/graphics/Makefile.am
--- EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre	2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/graphics/Makefile.am	2011-11-23 17:03:07.036953645 +0100
@@ -10,13 +10,12 @@ CYGWIN_LDAJAXG = -L../../plplot -L../exp
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
 endif
 
 
 AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/plplot \
--I$(top_srcdir)/ajax/pcre \
 $(EXTRA_INCLUDES)
 
 AJAXGSRC = ajgraph.c ajhist.c
diff -up EMBOSS-6.4.0/ajax/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/Makefile.am
--- EMBOSS-6.4.0/ajax/Makefile.am.system-pcre	2010-06-16 12:26:45.000000000 +0200
+++ EMBOSS-6.4.0/ajax/Makefile.am	2011-11-23 17:03:07.037953651 +0100
@@ -1,6 +1,6 @@
 ## Process this file with automake to produce Makefile.in
 if !ESYSTEMLIBS
-EXTRA_DIRS = expat zlib
+EXTRA_DIRS = expat zlib pcre
 endif
 
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
diff -up EMBOSS-6.4.0/configure.in.system-pcre EMBOSS-6.4.0/configure.in
--- EMBOSS-6.4.0/configure.in.system-pcre	2011-06-23 20:47:57.000000000 +0200
+++ EMBOSS-6.4.0/configure.in	2011-11-23 17:05:22.496688169 +0100
@@ -459,31 +459,6 @@ esac
 
 
 
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR=7
-PCRE_MINOR=9
-PCRE_DATE=11-Apr-2009
-PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR}
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION=0:1:0
-PCRE_POSIXLIB_VERSION=0:0:0
-
-
 dnl Define where the EMBOSS package is located
 AC_SUBST([AJAX_FIXED_ROOT])
 AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
@@ -667,6 +642,7 @@ AC_ARG_ENABLE([systemlibs],
   [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
 if test "${enable_systemlibs}" = "yes" ; then
   have_systemlibs=yes
+  AC_CHECK_LIB(pcre, pcre_compile)
 fi
 AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"])
 AC_SUBST([ESYSTEMLIBS])
@@ -832,7 +808,6 @@ AC_CONFIG_FILES([Makefile
                  ajax/ensembl/Makefile
                  ajax/expat/Makefile
                  ajax/graphics/Makefile
-                 ajax/pcre/Makefile
                  ajax/zlib/Makefile
                  doc/Makefile
                  doc/manuals/Makefile
diff -up EMBOSS-6.4.0/emboss/Makefile.am.system-pcre EMBOSS-6.4.0/emboss/Makefile.am
--- EMBOSS-6.4.0/emboss/Makefile.am.system-pcre	2011-07-08 18:46:55.000000000 +0200
+++ EMBOSS-6.4.0/emboss/Makefile.am	2011-11-23 17:03:07.038953657 +0100
@@ -102,12 +102,11 @@ wossdata wossinput wossname wossoperatio
 yank
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 endif
 
 AM_CPPFLAGS =  -I$(top_srcdir)/ajax/core \
 	-I$(top_srcdir)/nucleus \
-	-I$(top_srcdir)/ajax/pcre \
 	$(EXTRA_INCLUDES) \
 	$(AXIS2C_CPPFLAGS) \
 	-I$(top_srcdir)/ajax/graphics \
@@ -399,14 +398,14 @@ testplot_SOURCES = testplot.c
 treetypedisplay_SOURCES = treetypedisplay.c
 
 if !ESYSTEMLIBS
-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../ajax/pcre/libepcre.la
 endif
 
 LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
 	../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
 	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
 	$(EXTRA_LDS) \
-	../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
+	../plplot/libeplplot.la \
 	$(XLIB)
 
 pkgdata_DATA = $(EXTRA_DIST)
diff -up EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre EMBOSS-6.4.0/nucleus/Makefile.am
--- EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre	2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/nucleus/Makefile.am	2011-11-23 17:03:07.039953663 +0100
@@ -19,14 +19,14 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre
 -lezlib -leplplot
 else
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 endif
 endif
 
 
 AM_CPPFLAGS =  -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot \
 	$(X_CFLAGS) -I$(srcdir)/ \
-	-I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
+	-I$(top_srcdir)/ajax \
 	$(EXTRA_INCLUDES) \
 	-I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \