diff -up EMBOSS-6.1.0/ajax/ajreg.h.pcre EMBOSS-6.1.0/ajax/ajreg.h
--- EMBOSS-6.1.0/ajax/ajreg.h.pcre	2007-02-09 19:30:59.000000000 +0100
+++ EMBOSS-6.1.0/ajax/ajreg.h	2009-09-27 03:17:19.000000000 +0200
@@ -16,8 +16,8 @@ extern "C"
 #define ajreg_h
 
 #include "ajax.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
 
 #define AJREG_OVECSIZE 30
 
@@ -37,7 +37,7 @@ extern "C"
 ******************************************************************************/
 
 typedef struct AjSRegexp {
-    real_pcre *pcre;
+    struct real_pcre *pcre;
     pcre_extra *extra;
     int *ovector;
     const char* orig;
diff -up EMBOSS-6.1.0/ajax/Makefile.in.pcre EMBOSS-6.1.0/ajax/Makefile.in
--- EMBOSS-6.1.0/ajax/Makefile.in.pcre	2009-07-15 01:15:58.000000000 +0200
+++ EMBOSS-6.1.0/ajax/Makefile.in	2009-09-27 03:17:19.000000000 +0200
@@ -81,7 +81,7 @@ am__libajax_la_SOURCES_DIST = ajacd.c aj
 	ajphylo.c ajrange.c ajreg.c ajreport.c ajseq.c ajseqabi.c \
 	ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c ajsort.c \
 	ajstr.c ajsys.c ajtable.c ajtime.c ajtranslate.c ajtree.c \
-	ajutil.c ajvector.c pcre.c pcre_study.c pcreposix.c ajgraph.c \
+	ajutil.c ajvector.c \
 	ajhist.c
 am__objects_1 = ajacd.lo ajalign.lo ajarr.lo ajassert.lo ajbase.lo \
 	ajcall.lo ajcod.lo ajdan.lo ajdmx.lo ajdom.lo ajdomain.lo \
@@ -92,7 +92,7 @@ am__objects_1 = ajacd.lo ajalign.lo ajar
 	ajreport.lo ajseq.lo ajseqabi.lo ajseqdb.lo ajseqread.lo \
 	ajseqtype.lo ajseqwrite.lo ajsort.lo ajstr.lo ajsys.lo \
 	ajtable.lo ajtime.lo ajtranslate.lo ajtree.lo ajutil.lo \
-	ajvector.lo pcre.lo pcre_study.lo pcreposix.lo
+	ajvector.lo
 am__objects_2 = ajgraph.lo ajhist.lo
 @ISCYGWIN_FALSE@am_libajax_la_OBJECTS = $(am__objects_1)
 @ISCYGWIN_TRUE@am_libajax_la_OBJECTS = $(am__objects_1) \
@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
 HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -172,7 +171,7 @@ LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 #LDFLAGS = -no-undefined
-LIBS = 
+LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
-PCRE_DATE = @PCRE_DATE@
-PCRE_LIB_VERSION = @PCRE_LIB_VERSION@
-PCRE_MAJOR = @PCRE_MAJOR@
-PCRE_MINOR = @PCRE_MINOR@
-PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@
-PCRE_VERSION = @PCRE_VERSION@
-POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@
 RANLIB = @RANLIB@
 SED = @SED@
 SET_MAKE = @SET_MAKE@
@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@
 @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
 @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
 @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
-PCRELIBVERSION = @PCRE_LIB_VERSION@
-PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@
 INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) -DPREFIX=\"$(prefix)\" -I$(top_srcdir)/plplot $(POSIX_MALLOC_THRESHOLD) 
 AJAXSRC = ajacd.c ajalign.c ajarr.c ajassert.c \
 ajbase.c ajcall.c ajcod.c \
@@ -288,8 +278,7 @@ ajrange.c ajreg.c ajreport.c \
 ajseq.c ajseqabi.c ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c \
 ajsort.c ajstr.c ajsys.c \
 ajtable.c ajtime.c ajtranslate.c ajtree.c \
-ajutil.c ajvector.c \
-pcre.c pcre_study.c pcreposix.c
+ajutil.c ajvector.c
 
 AJAXGSRC = ajgraph.c ajhist.c
 include_HEADERS = ajax.h ajarch.h ajdefine.h \
@@ -303,9 +292,7 @@ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
 ajrange.h ajreg.h ajreport.h \
 ajseq.h ajseqabi.h ajseqdata.h ajseqdb.h ajseqread.h ajseqtype.h ajseqwrite.h \
 ajsort.h ajstr.h ajsys.h \
-ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h \
-pcre.h pcre_chartables.c pcre_config.h pcre_get.c pcre_printint.c \
-pcre_internal.h pcreposix.h
+ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
 
 @ISCYGWIN_FALSE@libajax_la_SOURCES = $(AJAXSRC)
 @ISCYGWIN_TRUE@libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC)
@@ -440,9 +427,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajtree.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajutil.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajvector.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre_study.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcreposix.Plo@am__quote@
 
 .c.o:
 @am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff -up EMBOSS-6.1.0/configure.pcre EMBOSS-6.1.0/configure
--- EMBOSS-6.1.0/configure.pcre	2009-07-15 01:15:56.000000000 +0200
+++ EMBOSS-6.1.0/configure	2009-09-27 03:21:32.000000000 +0200
@@ -16724,6 +16724,73 @@ _ACEOF
 
 fi
 
+{ echo "$as_me:$LINENO: checking for pcre_compile in -lpcre" >&5
+echo $ECHO_N "checking for pcre_compile in -lpcre... $ECHO_C" >&6; }
+if test "${ac_cv_lib_pcre_pcre_compile+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lpcre  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* 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 pcre_compile ();
+int
+main ()
+{
+return pcre_compile ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+         test -z "$ac_c_werror_flag" ||
+         test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_pcre_pcre_compile=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+        ac_cv_lib_pcre_pcre_compile=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_pcre_pcre_compile" >&5
+echo "${ECHO_T}$ac_cv_lib_pcre_pcre_compile" >&6; }
+if test "x$ac_cv_lib_pcre_pcre_compile" = x""yes; then
+  LIBS="-lpcre $LIBS"
+else
+  LIBS="$LIBS"
+fi
+
 
 if test "`uname`" = "FreeBSD" && ${with_pngdriver} != "no"; then
 { $as_echo "$as_me:$LINENO: checking for main in -liconv" >&5