<div dir="ltr">Dear group, <div><br></div><div>I want to retrieve the ancestral sequences via compara API.</div><div><br></div><div>So I used</div><div>







<p class="">my $mlss = $mlss_adaptor->fetch_by_method_link_type_species_set_name("EPO", "mammals");</p><p class="">my $slice = $slice_adaptor->fetch_by_region('toplevel', $seq_region, $seq_region_start, $seq_region_end);</p><p class="">my $genomic_align_blocks =$genomic_align_block_adaptor ->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss,  $slice);                                                           </p><p class="">(I also attached my script  below.)</p><p class="">But instead of ancestral sequences, I get multiple alignments of the current species. </p><p class="">which look like:</p><div>







<p class="">homo_sapiens/11/34888581-35077850           ------------------------------------------------------------</p>
<p class="">felis_catus/D1/90701788-90852536            gggaacagaacacagcatgagaccatgctcagaacagatttcattcaggggctataa-aa</p>
<p class="">canis_familiaris/18/32879322-33028613       aggaacagaatatagcatgatcacatactca-------attcattcagtggctatattaa</p>
<p class="">equus_caballus/12/1619359-1776531           aggaacagggtggtg--cgacccct---------------tcctggaggggacc--tc--</p>
<p class="">sus_scrofa/2/28305627-28477519              gggaaccgaacatggcatgattac----gtgatactgattctattcaggggctatattaa</p>
<p class="">ovis_aries/15/63610201-63792541             gggaacagaacatagcatgattattcactgtgtactgatttcattcaggggctatactaa</p>
<p class="">bos_taurus/15/66212217-66395858             gggaacagaacacagcacaattattccctgtatactgatttcattcaggggctatactaa</p>
<p class="">rattus_norvegicus/3/99477347-99634398       ------------------------------------------------------------</p>
<p class="">mus_musculus/2/102948690-103088848          ------------------------------------------------------------</p>
<p class="">oryctolagus_cuniculus/1/174190771-174392712 ------------------------------------------------------------</p>
<p class="">macaca_mulatta/14/36757737-36941679         ------------------------------------------------------------</p>
<p class="">papio_anubis/14/29787300-29976716           ------------------------------------------------------------</p>
<p class="">gorilla_gorilla/11/35459310-35656044        ------------------------------------------------------------</p>
<p class="">pan_troglodytes/11/34873765-35067421        ------------------------------------------------------------</p>
<p class="">pongo_abelii/11/34236125-34418629           ------------------------------------------------------------</p>
<p class="">callithrix_jacchus/11/98105861-98306401     ------------------------------------------------------------</p><p class="">But according to "<a href="http://uswest.ensembl.org/info/genome/compara/analyses.html#ancestral">http://uswest.ensembl.org/info/genome/compara/analyses.html#ancestral</a>"</p><p class="">"<span style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px"> Each ancestral sequence is named according to the derived extant species. For example, a sequence named Hsap, Ptro, Mmul corresponds to the ancestor of the </span><i style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px">Homo sapiens</i><span style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px">, </span><i style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px">Pan troglodytes</i><span style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px">, and</span><i style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px">Macaca mulatta</i><span style="color:rgb(85,85,85);font-family:'Luxi Sans',Helvetica,Arial,Geneva,sans-serif;font-size:12.6666669845581px;line-height:16px"> genomes.</span>"</p><p class="">Why am I not getting ancestral sequences? And how can I get ancestral sequences?</p><p class="">Thank you in advance.</p><p class="">Haiming</p></div></div></div>