<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>Hi Richard,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><DIV>[richard]</DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV><BR></DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV>These are the problems:</DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV>1) As I understand it this:</DIV><DIV><BR></DIV><DIV>my $wholeseq = Bio::SeqFeature::Generic->new (</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-start => 1,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-end => $refseq->length,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-display_name =>$refseq->display_name</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>);</DIV><DIV><BR></DIV><DIV>should display the name of the gene (CD133/Prominin1) near the top of image. </DIV><DIV>It doesn't, am I misunderstanding or is there an error in the code?</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The contents of a sequence object's display_name varies depending on the type of sequence record; for a sequence object created from a Genbank record, it's the value of the LOCUS field on the first line of the record.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you want the gene name, you'll have to dig it out of the feature table. If you look at the Genbank record for your first sequence, you'll see that under both the gene and CDS primary features, the HUGO gene abbreviation is stored under the "gene" secondary tag, and various synonyms are under the "note" and "product" secondary tags.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">LOCUS NM_006017 3794 bp mRNA linear PRI 17-NOV-2006</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">DEFINITION Homo sapiens prominin 1 (PROM1), mRNA.</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">ACCESSION NM_006017</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">VERSION NM_006017.1 GI:5174386</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">[...skipping irrelevant part of the Genbank record...]</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">FEATURES Location/Qualifiers</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> source 1..3794</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /organism="Homo sapiens"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /mol_type="mRNA"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="taxon:9606"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /chromosome="4"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /map="4p15.32"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> gene 1..3794</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /gene="PROM1"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /note="prominin 1; synonyms: AC133, CD133, PROML1,</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> MSTP061"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="GeneID:8842"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="HGNC:9454"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="HPRD:HPRD_05079"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="MIM:604365"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> CDS 38..2635</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /gene="PROM1"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /go_component="integral to plasma membrane [pmid 9389720];</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> membrane"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /go_process="response to stimulus; visual perception"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /note="hProminin; prominin (mouse)-like 1; hematopoietic</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> stem cell antigen"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /codon_start=1</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /product="prominin 1"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /protein_id="NP_006008.1"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="GI:5174387"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="GeneID:8842"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="HGNC:9454"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="HPRD:HPRD_05079"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> /db_xref="MIM:604365"</FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">[....more...]</FONT></FONT></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In your script, you grab the primary features between lines 34-60. You can grab the secondary feature you want with something like:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>[cribbed from the Feature-Annotation HOWTO]</DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">for my $feat_object ($seq_object->get_SeqFeatures) { </FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier"> push @ids, $feat_object->get_tag_values("gene") if ($feat_object->has_tag("gene")); </FONT></FONT></DIV><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Courier">}</FONT></FONT></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><DIV></DIV><DIV>2) In the quoted example the CDS is broken up into smaller regions which are </DIV><DIV>then linked together in example 6. This isn't happening in my code and I </DIV><DIV>think it should be, I get one solid block for the CDS. I don't understand why </DIV><DIV>this is because I'm not clear which parts of the feature table are used to </DIV><DIV>define where the CDS should be split. I think this is the relevant bit of </DIV><DIV>code:</DIV><DIV><BR></DIV><DIV>foreach my $alt_trans (keys %main) {</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>foreach my $tag (keys %{ $main{$alt_trans}{'features'} }) {</DIV><DIV><BR></DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>my $feature = $main{$alt_trans}{'features'}{$tag};</DIV><DIV><BR></DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>$panel->add_track($feature,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-glyph => 'generic',</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-bgcolor => $colors[$idx++ % @colors],</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-fgcolor => 'black',</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-font2color => 'black',</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-key => $alt_trans,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-bump => +1,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-height => 8,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-label => 1,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>-description => 1,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>) if ($tag eq 'CDS');</DIV><DIV><BR></DIV><DIV>}</DIV><DIV>}</DIV></BLOCKQUOTE></DIV><BR><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The problem here is that RefSeq mRNA records don't contain intron-exon boundary information. I think you'll have to get that from an assembly record. From the Entrez gene page for PROM1, I obtained a Genbank record for the PROM1 genomic locus:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><A href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000004.10&from=15578955&to=15686664&strand=2&dopt=gb">http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000004.10&from=15578955&to=15686664&strand=2&dopt=gb</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Saving that as 'PROM1.gb' (the suffix is important), and running the bp_embl2picture.pl script on it, I got an image similar to Figure 6 (attached).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Hope this helps,</DIV><DIV>Dave</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><IMG src="cid:ADD8BADA-4501-4E92-8F8F-2F858748208D@local"></DIV></BODY></HTML>