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Hello,</div>
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I was wondering if it is possible to extract ancestral sequences from the EPO MSA such as those that are returned in the browser when looking up a multiple alignment for a given region, ie. </div>
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Ancestral sequences 15 › ((((((homo_sapiens,(pan_paniscus,pan_troglodytes)),gorilla_gorilla),pongo_abelii),(chlorocebus_sabaeus,((macaca_fascicularis,macaca_mulatta),(papio_anubis,theropithecus_gelada)))),((microtus_ochrogaster,((mus_caroli,mus_pahari),rattus_norvegicus)),oryctolagus_cuniculus)),(((((((bos_grunniens,(bos_indicus_hybrid,(bos_tauruse-05,bos_taurus))),(ovis_aries,ovis_aries_rambouillet)),cervus_hanglu_yarkandensis),physeter_catodon),(catagonus_wagneri,sus_scrofa)),(((canis_lupus_dingoe-05,(canis_lupus_familiaris,canis_lupus_familiarisgreatdanee-05)e-05),(ursus_thibetanus_thibetanus,zalophus_californianus)),(((felis_catus,lynx_canadensis),(panthera_leo,panthera_pardus)),suricata_suricatta))),equus_caballus));<br>
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We are currently using the compara perl API (for ensembl/compara v102) to retrieve aligned (gapped) sequences from genomic_align objects as below. <br>
<span style="margin:0px;font-size:12pt">Is there any way to retrieve ancestral the above ancestral sequences in similar fashion? If so, which mysql tables need to be installed?</span></div>
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<span style="margin:0px;font-size:12pt"><span class="pl-k" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">my</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">
</span><span style="margin:0px;font-size:12pt"><span class="pl-smi" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">$method_link_species_set_adaptor</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">
= Bio::EnsEMBL::Registry</span><span style="margin:0px;font-size:12pt"><span class="pl-k" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">-></span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">get_adaptor(</span><span style="margin:0px;font-size:12pt"><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span><span class="pl-s" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">Multi</span><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">,
</span><span style="margin:0px;font-size:12pt"><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span><span class="pl-s" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">compara</span><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">,
</span><span style="margin:0px;font-size:12pt"><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span><span class="pl-s" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">MethodLinkSpeciesSet</span><span class="pl-s"><span class="pl-pds" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">'</span></span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">);</span><span style="margin:0px;font-size:12pt"><br>
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<span style="margin:0px;font-size:12pt"><span class="pl-k" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">my</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">
</span><span style="margin:0px;font-size:12pt"><span class="pl-smi" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">$method_link_species_set</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">
= </span><span style="margin:0px;font-size:12pt"><span class="pl-smi" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">$method_link_species_set_adaptor</span><span class="pl-k" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">-></span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">fetch_by_method_link_type_species_set_name(</span><span style="margin:0px;font-size:12pt"><span class="pl-smi" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">"EPO"</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">,
</span><span style="margin:0px;font-size:12pt"><span class="pl-smi" style="font-family: Consolas, Courier, monospace; font-size: 11pt;">"mammals"</span></span><span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;">);</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"><span class="pl-k">my</span>
<span class="pl-smi">$slice_adaptor</span> = Bio::EnsEMBL::Registry<span class="pl-k">-></span>get_adaptor('mus_musculus',
<span class="pl-s"><span class="pl-pds">'</span>core<span class="pl-pds">'</span></span>,
<span class="pl-s"><span class="pl-pds">'</span>Slice<span class="pl-pds">'</span></span>);<br>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"><span class="pl-k">my</span>
<span class="pl-smi">$genomic_align_block_adaptor</span> = Bio::EnsEMBL::Registry<span class="pl-k">-></span>get_adaptor(<span class="pl-s"><span class="pl-pds">'</span>Multi<span class="pl-pds">'</span></span>,
<span class="pl-s"><span class="pl-pds">'</span>compara<span class="pl-pds">'</span></span>,
<span class="pl-s"><span class="pl-pds">'</span>GenomicAlignBlock<span class="pl-pds">'</span></span>);<br>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"># peak information taken from a bed file of ChiP-seq peaks</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"><span class="pl-k">my</span>
<span class="pl-smi">$query_slice</span> = <span class="pl-smi">$slice_adaptor</span><span class="pl-k">-></span>fetch_by_region(<span class="pl-s"><span class="pl-pds">'</span>toplevel<span class="pl-pds">'</span></span>,
<span class="pl-smi">$peak_chr</span>, <span class="pl-smi">$peak_start</span>, <span class="pl-smi">
$peak_end</span>);<br>
</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"><span class="pl-k">my</span>
<span class="pl-smi">$genomic_align_blocks</span> = <span class="pl-smi">$genomic_align_block_adaptor</span><span class="pl-k">-></span>fetch_all_by_MethodLinkSpeciesSet_Slice(<span class="pl-smi">$method_link_species_set</span>,
<span class="pl-smi">$query_slice</span>);<br>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"><span class="pl-k">foreach</span>
<span class="pl-k">my</span> <span class="pl-smi">$this_genomic_align_block</span> (<span class="pl-smi">@$genomic_align_blocks</span>) {<br>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> <span class="pl-k">my</span>
<span class="pl-smi">$genomic_align_array</span> = <span class="pl-smi">$this_genomic_align_block</span><span class="pl-k">-></span>genomic_align_array();</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> <span class="pl-k">foreach</span>
<span class="pl-k">my</span> <span class="pl-smi">$genomic_align</span> (<span class="pl-smi">@$genomic_align_array</span>) {</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> if ((List::MoreUtils::first_index { $_ eq $genomic_align->genome_db()->name() } @dbnames_used) != -1) {</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> # Loops thru each species present in the genomic_align and only process if matching a predefined list of species used<br>
# example @dbnames: canis_lupus_familiaris,homo_sapiens,mus_musculus</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> <span class="pl-k">my</span>
<span class="pl-smi">$genome_id</span>=<span class="pl-smi">$genomic_align</span><span class="pl-k">-></span>genome_db()<span class="pl-k">-></span>name();</span></div>
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<span style="margin: 0px; font-size: 11pt; font-family: Consolas, Courier, monospace;"> <span class="pl-smi">$orthologous_sequences</span>{<span class="pl-smi">$query_peak</span>}<span class="pl-k">-></span>{<span class="pl-smi">$genome_id</span>} =
<span class="pl-smi">$genomic_align</span><span class="pl-k">-></span>aligned_sequence();</span></div>
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<span style="margin:0px;font-size:12pt">Thanks in advance!</span></div>
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<span style="margin:0px;font-size:12pt">Minggao (Michael) Liang</span></div>
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