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<p class="MsoNormal"><span style="font-size:11.0pt">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve been trying to retrieve some GRCh37 protein sequences with code similar to that below and have found some proteins that have corrupted sequences, including asterisks. Please can you tell me how to get
the correct protein sequences?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="p1"><span class="s1">#!/usr/bin/env perl</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p3"><span class="s2">use</span><span class="s1"> strict;</span><o:p></o:p></p>
<p class="p3"><span class="s2">use</span><span class="s1"> warnings;</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p3"><span class="s2">use</span><span class="s1"> Bio::EnsEMBL::Registry;</span><o:p></o:p></p>
<p class="p3"><span class="s2">use</span><span class="s1"> Getopt::Long qw(GetOptionsFromArray);</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p4"><span class="s2">my</span><span class="s3"> $registry = </span><span class="s1">'Bio::EnsEMBL::Registry'</span><span class="s3">;</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p3"><span class="s1">$registry->load_registry_from_db(</span><o:p></o:p></p>
<p class="p4"><span class="apple-converted-space"> </span><span class="s3">-host =>
</span><span class="s1">'ensembldb.ensembl.org'</span><span class="s3">,</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s1">-user =>
</span><span class="s4">'anonymous'</span><span class="s1">,</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s1">-port =>
</span><span class="s4">'3337'</span><o:p></o:p></p>
<p class="p3"><span class="s1">);</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p3"><span class="s2">my</span><span class="s1"> $transcript_adaptor = $registry->get_adaptor(
</span><span class="s4">'Human'</span><span class="s1">, </span><span class="s4">'otherfeatures'</span><span class="s1">,
</span><span class="s4">'Transcript'</span><span class="s1"> );</span><o:p></o:p></p>
<p class="p3"><span class="s2"><o:p> </o:p></span></p>
<p class="p3"><span class="s2">foreach</span><span class="s1"> </span><span class="s2">my</span><span class="s1"> $transcript_id (</span><span class="s4">"NM_002426.4"</span><span class="s1">) {</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s2">foreach</span><span class="s1">
</span><span class="s2">my</span><span class="s1"> $transcript (@{ $transcript_adaptor->fetch_all_versions_by_stable_id($transcript_id) }) {</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s2">my</span><span class="s1"> $protein = $transcript->translation();</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s2">defined</span><span class="s1">($protein)
</span><span class="s2">or</span><span class="s1"> </span><span class="s2">next</span><span class="s1">;</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s2">print</span><span class="s1">
</span><span class="s4">">"</span><span class="s1"> . $protein->stable_id() . </span>
<span class="s4">"\n"</span><span class="s1">;</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s2">print</span><span class="s1"> $protein->seq() .
</span><span class="s4">"\n"</span><span class="s1">;</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><span class="s1">}</span><o:p></o:p></p>
<p class="p3"><span class="s1">}</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Luke</span><o:p></o:p></p>
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