diff --git a/scripts/Analysis/find_supporting_evidence b/scripts/Analysis/find_supporting_evidence
new file mode 100755
index 0000000000000000000000000000000000000000..1ac3f9e813218b28097aab28a0a20573a982df7b
--- /dev/null
+++ b/scripts/Analysis/find_supporting_evidence
@@ -0,0 +1,140 @@
+#!/usr/local/bin/perl
+
+BEGIN {
+ unshift (@INC,"/nfs/disk89/michele/bioperl-live");
+ unshift (@INC,"/nfs/disk89/michele/pogdir/ensembl/modules");
+}
+
+# Let the code begin...
+
+
+use Bio::EnsEMBL::DBSQL::Obj;
+use Bio::EnsEMBL::TimDB::Obj;
+use Bio::EnsEMBL::DB::ContigI;
+
+use Getopt::Long;
+use strict;
+
+my ($dbname,
+ $dbhost,
+ $dbuser,
+ $dbpass,
+ $clonefile,
+ );
+
+$|=1;
+
+GetOptions("dbname=s" => \$dbname,
+ "dbhost=s" => \$dbhost,
+ "dbuser=s" => \$dbuser,
+ "dbpass=s" => \$dbpass,
+ "clonefile=s" => \$clonefile,
+ ) or usage();
+
+$dbname = 'ensembl' unless $dbname;
+$dbhost = 'obi-wan' unless $dbhost;
+$dbuser = 'ens-ro' unless $dbuser;
+$dbpass = '' unless $dbpass;
+# Connect to the database
+
+my $db = Bio::EnsEMBL::DBSQL::Obj->new(-dbname => $dbname,
+ -host => $dbhost,
+ -user => $dbuser,
+ -pass => $dbpass,
+ ) or die "Can't connect to database";
+
+my $db2 = Bio::EnsEMBL::DBSQL::Obj->new(-dbname => 'ensembl',
+ -host => $dbhost,
+ -user => $dbuser,
+ -pass => $dbpass,
+ ) or die "Can't connect to database";
+
+my @clones = get_clones($clonefile);
+
+
+foreach my $cloneid (@clones) {
+ eval {
+ print(STDERR " - Processing clone $cloneid\n");
+ my $clone = $db->get_Clone($cloneid);
+ print(STDERR " - getting genes for clone $cloneid\n");
+
+ my @features;
+
+ print(STDERR " - getting contigs\n");
+
+ foreach my $contig ($clone->get_all_Contigs) {
+ push(@features,$contig->get_all_SimilarityFeatures);
+ }
+
+ print(STDERR " - getting genes\n");
+ my @genes = $clone->get_all_Genes;
+ print(STDERR " - done\n");
+
+ foreach my $gene (@genes) {
+
+ print(STDERR " - processing gene " . $gene->id . "\n");
+
+ foreach my $exon ($gene->each_unique_Exon) {
+
+ my @homols;
+
+ print(STDERR " - processing exon " . $exon->id . "\n");
+
+ $exon ->find_supporting_evidence (\@features);
+ print(STDERR " - found supporting evidence\n");
+ $db2 ->write_supporting_evidence($exon);
+ }
+ }
+ };
+ if ($@) {
+ print(STDERR "Error processing clone $cloneid. Skipping clone");
+ }
+}
+
+############################################################
+#
+# Subroutines.
+#
+# This are inserted mostly just for tidiness
+#
+############################################################
+
+sub usage {
+ print("\nUsage: featureparser_test2 <clone> <contig_number> <accession>\n");
+ exit(0);
+}
+
+sub get_clones {
+ my ($clonefile) = @_;
+
+ open(FILE,"<$clonefile") || die "Can't open clone file $clonefile";
+
+ my @clones;
+ while (<FILE>) {
+ chomp;
+ push(@clones,$_);
+ }
+
+ return @clones;
+}
+
+sub homol2gff {
+ my ($fh,$homols,$exon) = @_;
+
+ foreach my $h1 (@$homols) {
+ my $h2 = $h1->feature2;
+ my $strand = "+";
+
+ if ($h2->strand == -1) {
+ $strand = "-";
+ }
+
+ print($fh $exon . "\t" . $h1->source_tag . "\t" . $h2->primary_tag ."\t" . $h1->start . "\t" . $h1->end . "\t" . $h1->score ."\t" . $strand .
+ "\t0\tSequence:" .
+ $h2->seqname . "\t" . $h2->start . "\t" . $h2->end ."\n");
+ }
+}
+
+
+
+
diff --git a/scripts/Analysis/supporting_evidence_test b/scripts/Analysis/supporting_evidence_test
new file mode 100755
index 0000000000000000000000000000000000000000..9839c9c4af1739a9038c831bfac156b667ac288b
--- /dev/null
+++ b/scripts/Analysis/supporting_evidence_test
@@ -0,0 +1,114 @@
+#!/usr/local/bin/perl
+
+BEGIN {
+ unshift (@INC,"/nfs/disk89/michele/bioperl-live");
+ unshift (@INC,"/nfs/disk89/michele/pogdir/ensembl/modules");
+}
+
+# Let the code begin...
+
+
+use Bio::EnsEMBL::DBSQL::Obj;
+use Bio::EnsEMBL::TimDB::Obj;
+use Bio::EnsEMBL::DB::ContigI;
+
+use Getopt::Long;
+use strict;
+
+my ($cloneid,
+);
+
+$|=1;
+
+GetOptions("clone=s" => \$cloneid, # Clone name e.g. dJ998N21
+ ) or usage();
+
+# Connect to the database
+
+my $db = Bio::EnsEMBL::DBSQL::Obj->new(-dbname => 'pogtest',
+ -host => 'obi-wan',
+ -user => 'ensloader',
+ ) or die "Can't connect to database";
+my @clones;
+push(@clones,$cloneid);
+
+my $clone = $db->get_Clone($cloneid);
+print(" - getting genes for clone $cloneid\n");
+
+open(POG,">" . $clone->id . ".gff");
+
+
+my @homols;
+my @features;
+
+print(" - getting contigs\n");
+
+foreach my $contig ($clone->get_all_Contigs) {
+ push(@features,$contig->get_all_SimilarityFeatures);
+}
+
+print(" - getting genes\n");
+my @genes = $clone->get_all_Genes;
+print(" - done\n");
+
+foreach my $gene (@genes) {
+
+ print(" - processing gene " . $gene->id . "\n");
+
+ foreach my $exon ($gene->each_unique_Exon) {
+ my @homols;
+ print(" - processing exon " . $exon->id . "\n");
+ $exon ->find_supporting_evidence (\@features);
+ print(" - found supporting evidence\n");
+ $db ->write_supporting_evidence($exon);
+
+ $exon->{_supporting_evidence} = [];
+ print("supporting features are [" . $exon->each_Supporting_Feature . "]\n");
+ print(" - written supporting evidence\n");
+ $db ->get_supporting_evidence ($exon);
+ print(" - got supporting evidence\n");
+ push(@homols,$exon->each_Supporting_Feature);
+ homol2gff(\*POG,\@homols,$exon->id); # Prints out gff.
+ }
+ }
+
+
+
+
+close(POG);
+
+
+############################################################
+#
+# Subroutines.
+#
+# This are inserted mostly just for tidiness
+#
+############################################################
+
+sub usage {
+ print("\nUsage: featureparser_test2 <clone> <contig_number> <accession>\n");
+ exit(0);
+}
+
+
+sub homol2gff {
+ my ($fh,$homols,$exon) = @_;
+
+ foreach my $h1 (@$homols) {
+ my $h2 = $h1->feature2;
+ my $strand = "+";
+
+ if ($h2->strand == -1) {
+ $strand = "-";
+ }
+
+ print($fh $exon . "\t" . $h1->source_tag . "\t" . $h2->primary_tag ."\t" . $h1->start . "\t" . $h1->end . "\t" . $h1->score ."\t" . $strand .
+ "\t0\tSequence:" .
+ $h2->seqname . "\t" . $h2->start . "\t" . $h2->end ."\n");
+ }
+}
+
+
+
+
diff --git a/scripts/Analysis/testHMM b/scripts/Analysis/testHMM
new file mode 100755
index 0000000000000000000000000000000000000000..a85e058c7293dac0eba55f9adb57f7f6a8798b0e
--- /dev/null
+++ b/scripts/Analysis/testHMM
@@ -0,0 +1,100 @@
+#!/usr/local/bin/perl
+
+BEGIN {
+ unshift (@INC,"/nfs/disk89/michele/bioperl-live");
+ unshift (@INC,"/nfs/disk89/michele/pogdir/ensembl/modules");
+}
+
+# Let the code begin...
+
+
+use Bio::EnsEMBL::Analysis::Genscan;
+use Bio::EnsEMBL::Analysis::GenscanPeptide;
+use Bio::Tools::HMMER::Results;
+
+use Getopt::Long;
+use strict;
+
+my ($clone,
+ $contig,
+);
+
+
+GetOptions("clone=s" => \$clone, # Clone name e.g. dJ998N21
+ "contig=s" => \$contig, # Contig number e.g. 00577
+ ) or usage();
+
+# Initialize directories and clone/contig names
+
+my $root_dir = "/nfs/disk100/humpub/th/unfinished_ana/data/$clone/";
+
+my $gsfile = $root_dir . "/" . $clone . "." . $contig . ".gs";
+my $dnafile = $root_dir . "/" . $clone . ".seq";
+
+
+open(POG,">$clone.$contig.gff"); # This is for gff output
+
+my $fh = \*POG;
+my $dna = find_seq($dnafile,$clone,$contig) or die "Couldn't find dna for $clone.$contig";
+my $gs = new Bio::EnsEMBL::Analysis::Genscan($gsfile,$dna);
+
+my $count = 0;
+
+TRANS: foreach my $g ($gs->each_Transcript) {
+
+ $count++;
+
+ print_gene($fh,$g); # Just for debugging purposes
+
+ my $genpep = new Bio::EnsEMBL::Analysis::GenscanPeptide($g);
+
+ my $pfamfile = $root_dir . "/" . $clone . "." . $contig . ".$count.hmmpfam_frag";
+ print("Pfamfile is $pfamfile\n");
+
+ my $res = new Bio::Tools::HMMER::Results( -file => "$pfamfile",
+ -type => 'hmmpfam');
+
+ print("Made object\n");
+ # print out the results for each sequence
+ foreach my $seq ( $res->each_Set ) {
+ print("here\n");
+ print "Sequence bit score is",$seq->bits,"\n";
+ foreach my $domain ( $seq->each_Domain ) {
+ print " Domain start ",$domain->start," end ",$domain->end," score ",$domain->bits,"\n";
+ }
+ }
+
+ # new result object on a sequence/domain cutoff of 25 bits sequence, 15 bits domain
+# my $newresult = $res->filter_on_cutoff(25,15);
+
+ # alternative way of getting out all domains directly
+ foreach my $domain ( $res->each_Domain ) {
+ print "Domain on ",$domain->seqname," with score ",$domain->bits," evalue ",$domain->evalue,"\n";
+ }
+}
+sub find_seq {
+ my ($dnafile,$clone,$contig) = @_;
+
+ my $seqio = new Bio::SeqIO(-file => $dnafile,
+ -format => 'Fasta');
+
+ my $dna;
+
+ while (my $d = $seqio->next_seq) {
+ if ($d->id eq "$clone.$contig") {
+ $dna = $d;
+ }
+ }
+ return $dna;
+}
+sub print_gene {
+ my ($fh,$g) = @_;
+
+ foreach my $ex ($g->each_Exon) {
+ print($fh "Gene\tGENSCAN\texon\t" . $ex->start . "\t" . $ex->end . "\t0\t" . $ex->strand . "\t0\n");
+ }
+
+ print("\nTranslation " . $g->translate()->seq . "\n");
+}
+
+