--- meme_3.5.4/website/cgi-bin/meme.pl	2006-09-21 19:46:29.000000000 +0000
+++ trunk/website/cgi-bin/meme.pl	2007-09-10 00:28:33.000000000 +0000
@@ -1,6 +1,6 @@
 #!@WHICHPERL@
 ##
-## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
 ##
 ## $Log: meme-3.5.4-patch2.patch,v $
 ## Revision 1.1  2007/09/17 02:41:56  je_fro
 ## Add upstream patches and disable parallel install on amd64.
 ## (Portage version: 2.1.3.9)
 ##
 ## Revision 1.12  2006/03/07 23:30:19  nadya
@@ -467,21 +467,21 @@
 
   # check against allowed dna letters
   $x = $_;
-  $x =~ tr/ABCDGHKMNRSTUVWY//cd;
+  $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
   $new = length $x;
   if ($old == $new) {
     "dna";
   } else {
     # check against allowed protein letters
     $x = $_;
-    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
+    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
     $new = length $x;
     if ($old == $new) {
       "protein";
     } else {
       # get the unknown letters
       $x = $_;
-      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
+      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
       &whine("
 	Your sequences contained the following unrecognized letters: $x.
 	<BR>
--- meme_3.5.4/website/cgi-bin/mast.pl	2006-09-21 19:46:29.000000000 +0000
+++ trunk/website/cgi-bin/mast.pl	2007-09-10 00:38:14.000000000 +0000
@@ -1,6 +1,6 @@
 #!@WHICHPERL@
 ##
-## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
 ##
 ## $Log: meme-3.5.4-patch2.patch,v $
 ## Revision 1.1  2007/09/17 02:41:56  je_fro
 ## Add upstream patches and disable parallel install on amd64.
 ## (Portage version: 2.1.3.9)
 ##
 ## Revision 1.8  2006/03/07 23:30:19  nadya
@@ -479,21 +479,21 @@
 
   # check against allowed nucleotide letters
   $x = $_;
-  $x =~ tr/ABCDGHKMNRSTUVWY//cd;
+  $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
   $new = length $x;
   if ($old == $new) {
     return("DNA");
   } else {
     # check against allowed protein letters
     $x = $_;
-    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
+    $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
     $new = length $x;
     if ($old == $new) {
       return("PROTEIN");
     } else {
       # get the unknown letters
       $x = $_;
-      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
+      $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
       &whine("
         Your sequences contained the following unrecognized letters: $x.
         <BR>