diff --git a/getDomainTopology.pl b/getDomainTopology.pl
index fd02b6e..ecce9e5 100755
--- a/getDomainTopology.pl
+++ b/getDomainTopology.pl
@@ -234,6 +234,12 @@ sub prepare_seqs_for_projection {
   my $tcdbDir = "$rootDir/tcdb";
   system "mkdir -p $tcdbDir" unless (-d $tcdbDir);
 
+  #to prevent modifying the original files, here I'll save the input
+  #sequences with the artificial TCIDs
+  my $origInfilesDir = "$rootDir/inputFiles";
+  system "mkdir -p $origInfilesDir" unless (-d $origInfilesDir);
+
+
   #generate an empty "TCDB sequence file" that will contains proteins not in TCDB
   my $new_tcdbSeqsFile = "$tcdbDir/tcdb.faa";
   system "cat /dev/null > $new_tcdbSeqsFile";
@@ -247,6 +253,8 @@ sub prepare_seqs_for_projection {
     my $tcid = $pair->[0];
     my $tgtF = $pair->[1];
 
+    my @comp = split(/\//, $tgtF);
+    my $tgtFileName = $comp[-1];
 
     #Add family to the main array (as if provided by the -f commandline option)
     push (@fams, $tcid);
@@ -270,8 +278,8 @@ sub prepare_seqs_for_projection {
 
 
     #Replace the TCID in the file corresponding to the target proteins
-    my $cmd1 = qq(perl -i.orig -pe 's/\\>([a-zA-Z0-9_-]+).*/\\>${tgtTC}-\$1/;' $tgtF);
-    system $cmd1 unless (-f "${tgtF}.orig");
+    my $cmd1 = qq(perl -pe 's/\\>([a-zA-Z0-9_-]+).*/\\>${tgtTC}-\$1/;' $tgtF > $origInfilesDir/$tgtFileName);
+    system $cmd1 unless (-f "$origInfilesDir/$tgtFileName");
 
 
     #Extract sequences for reference family
@@ -282,7 +290,7 @@ sub prepare_seqs_for_projection {
 
 
     #Add family and target sequences to the new TCDB family
-    my $cmd3 = qq(cat $outFile $tgtF >> $new_tcdbSeqsFile);
+    my $cmd3 = qq(cat $outFile $origInfilesDir/$tgtFileName >> $new_tcdbSeqsFile);
     system $cmd3;
   }