<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Menlo;
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Users wishing to retrieve sequences from assembly versions in previous releases of Ensembl might be interested in using the JEnsembl Java API.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">( freely available from
<a href="http://jensembl.sourceforge.net/">http://jensembl.sourceforge.net/</a> )
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">One of the useful features of JEnsembl is its backwards compatibility and version awareness.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Code example using the current release 75 of JEnsembl (release 76 is coming soon...)
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">DBRegistry eReg = DBRegistry.createRegistryForDataSource(DBConnection.DataSource.ENSEMBLDB);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">DBSpecies mouse = eReg.getSpeciesByAlias("mouse");<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> System.out.println("Release 67 Assembly is " +mouse.getAssemblyName("67"));<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">DAChromosome chr7v67 = mouse.getChromosomeByName("7", "67");<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">System.out.println("chr7v67 (123336212-123338053): "+chr7v67.getSequenceAsString(123336212 , 123338053 ));<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">System.out.println("Release 75 Assembly is " +mouse.getAssemblyName("75"));<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">DAChromosome chr7v75 = mouse.getChromosomeByName("7", "75");<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">System.out.println("chr7v75 (123336212-123338053): "+chr7v75.getSequenceAsString(123336212 , 123338053 ));<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Outputs<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Release 67 Assembly is NCBIM37<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">chr7v67 (123336212-123338053): TCCATTGAGAAAGGAGACAGGCCTGCAGGGAT … etc<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Release 75 Assembly is GRCm38.p2<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">chr7v75 (123336212-123338053): AGGTGCACACTCTGTAAGGAAGGAAACCCAGT … etc<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">JEnsembl can connect to any Ensembl datasource including those hosted by Ensembl and EnsemblGenomes (invertebrates, plants, bacteria etc…)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Trevor Paterson PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><a href="mailto:trevor.paterson@roslin.ed.ac.uk"><span style="color:blue">trevor.paterson@roslin.ed.ac.uk</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Bioinformatics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">The Roslin Institute<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Royal (Dick) School of Veterinary Studies
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">University of Edinburgh
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Easter Bush<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Midlothian<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">EH25 9RG<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Scotland UK<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">phone +44 (0)131 651 9157<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><a href="http://bioinformatics.roslin.ed.ac.uk/"><span style="color:blue">http://bioinformatics.roslin.ed.ac.uk/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland
with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-left:36.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Ashley Waardenberg<br>
<b>Sent:</b> 21 August 2014 07:13<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> [ensembl-dev] getting sequences from older assemblies using the Perl API<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">If I select any other assembly version (below as variable "$version") other than the highest ranked, I seem to only get "N" as sequences
returned. I have tried this for both mouse and human. This is using the perl API version 75, below is an example querying a sequence at some specific coordinate. If I retrieve the soft-masked region, it returns lower cases where expected, but is still all
"n". If I change the assembly to highest rank (e.g. GRCm38) it retrieves "proper" sequence, but obviously at the wrong coordinates as I am using NCBIM37 fragments.<o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Is this a possible bug/any ideas?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Ash<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">#code start<o:p></o:p></span></p>
</div>
<div>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">use</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> Bio::EnsEMBL::Registry;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span></span><span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $registry =
</span></span><span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"Bio::EnsEMBL::Registry"</span></span><span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">;</span></span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $species =
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"mouse"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $version =
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"NCBIM37"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">$registry->load_registry_from_db( <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> -host =>
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">'ensembldb.ensembl.org'</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">, </span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> -user =>
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">'anonymous'</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">);<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $adaptor = $registry->get_adaptor($species,</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">'Core'</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">,</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">'Slice'</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">);<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#008423">#slice of interest:</span></span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $slice = $adaptor->fetch_by_region(</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">'chromosome'</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">,
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#2F2FD1">7</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> ,
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#2F2FD1">123336212</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> ,
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#2F2FD1">123338053</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> ,
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#2F2FD1">1</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">, $version);<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span class="apple-style-span"><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#008423">#different elements of the slice:</span></span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $sequence = $slice->seq();<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $softmasked = $slice->get_repeatmasked_seq(
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">undef</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">,
</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#2F2FD1">1</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> );<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">my</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $softmasked_seq = $softmasked->seq();<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt;min-height: 13px">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#008423">#print sliced sequences:<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">print</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $sequence.</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"\n"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">.</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"\n"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">.</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"\n"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:#BE299D">print</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"> $softmasked_seq.</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:#D42722">"\n"</span><span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">;<o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif"">#code end<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
</div>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black">#this prints the following out:<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif";color:black"><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif"">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif""><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif""><o:p> </o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt;margin-bottom:.0001pt">
<span style="font-size:8.5pt;font-family:"Menlo","serif"">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN<o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif""><br>
______________________________________________________________________<br>
The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.<o:p></o:p></span></p>
</div>
</body>
</html>