diff --git a/misc-scripts/protein_match/get_Xmapping.pl b/misc-scripts/protein_match/get_Xmapping.pl
index e46fc41a2d0b2873396149aefde98dce1be1e98b..8442eabf14b1d35aeac974e74d4720eec390afdf 100644
--- a/misc-scripts/protein_match/get_Xmapping.pl
+++ b/misc-scripts/protein_match/get_Xmapping.pl
@@ -321,17 +321,17 @@ if ($organism eq "human") {
 #Get Xref mapping specifically for mouse.
 if ($organism eq "mouse") {
     my %mgi2sp;
+    # 20/02/04:th MGI changed files for MGI to SP mappings.  File format also changed
+    # moving $sps from 6th to 7th column.
     open (MGISP, "$mgi_sp") || die "Can't open $mgi_sp\n";
     while (<MGISP>) {
-	chomp;
-	my ($mgi,$rik,$a,$b,$c,$sps) = split (/\t/,$_);
-      	
-	my @sp = split(/\s/,$sps);
-	
-	#put in hash all of the SP entries which correspond to an MGI (this will be used later)
-	$mgi2sp{$mgi} = $sps;
-	
+      chomp;
+      my ($mgi,$rik,$a,$b,$c,$d,$sps) = split (/\t/,$_);
+      my @sp = split(/\s/,$sps);
+      #put in hash all of the SP entries which correspond to an MGI (this will be used later)
+      $mgi2sp{$mgi} = $sps;
     }
+    close MGISP;
     open (MGILOC, "$mgi_locus") || die "Can't open $mgi_locus\n";
     my %mgi_got;
     my %mgi_syns;
@@ -348,9 +348,9 @@ if ($organism eq "mouse") {
 	}	    
       }else{
 	$mgi_got{$mgi} = $locus;
-      }
-      
+      }      
     }
+    close MGILOC;
 	
     my @mgi_ids = keys(%mgi_got);
     foreach my $mgi(@mgi_ids){
diff --git a/misc-scripts/protein_match/mapping_conf.pl.example b/misc-scripts/protein_match/mapping_conf.pl.example
index ca100d475d6fb1b1278cc175360dde0441ebd7eb..83b6c45382b060fbd122f507ef062243e2c43e53 100644
--- a/misc-scripts/protein_match/mapping_conf.pl.example
+++ b/misc-scripts/protein_match/mapping_conf.pl.example
@@ -122,8 +122,9 @@ package main;
                   #The files needed for the mouse X_mapping can be obatained there: ftp://ftp.informatics.jax.org/pub/reports/   
                   #2 files are needed MRK_SwissProt.rpt and MRK_LocusLink.rpt
                   
-                   #File containing MGI/SP mapping (MRK_SwissProt.rpt)
-                   #'mgi_sp'  => '/work1/mongin/mouse/mapping/primary/MRK_SwissProt.rpt',                 
+                   #File containing MGI/SP mapping (MRK_SwissProt_TrEMBL.rpt)
+		   #(20/02/04:th: file format changed, so get_Xmapping.pl changed at this point)
+                   #'mgi_sp'  => '/work1/mongin/mouse/mapping/primary/MRK_SwissProt_TrEMBL.rpt',                 
                    'mgi_sp'  => '',
                   
                    #File containing MGI/LocusLink mapping (MRK_LocusLink.rpt)