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Hi Duarte,<br>
<br>
Historically, Ensembl only supports one assembly for a species at a
given time.<br>
<br>
Storing sequence for more than one assembly could lead to undesired
consequences.<br>
For example, contigs being shared between assemblies, we will end up
with contigs which are not part of the current assembly, but
necessary to provide sequence for the previous assembly.<br>
<br>
We are aware though that this could prove incredibly useful.<br>
To test those changes, we have loaded the additional data in the
human database used for the REST server.<br>
It is now possible to retrieve sequence for any past or present
human assembly (back to NCBI34)<br>
<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta">http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta</a><br>
or<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta;coord_system_version=GRCh38">http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta;coord_system_version=GRCh38</a><br>
will return the sequence for chromosome 2 in GRCh38<br>
<br>
while<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta;coord_system_version=GRCh37">http://rest.ensembl.org/sequence/region/human/2:3118382-3127806?content-type=text/x-fasta;coord_system_version=GRCh37</a><br>
will return the sequence for chromosome 2 in GRCh37<br>
<br>
Please try it out and let us know if you find any issues with this.<br>
<br>
If this is successfull, we will consider extending this to the main
human databases, which means you would be able to retrieve sequence
for previous assemblies via the API.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 07/10/2014 11:13, Duarte Molha
wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoE+C2UBPnpF-fgSjp2JjhvzrX2mGK==Ru2xj-kGR_P7BoQ@mail.gmail.com"
type="cite">
<div dir="ltr">Any chance you might consider implementing this?
<div>I think it would be very useful to be able to retrieve the
underlying sequence in previous assemblies since the transform
method can already give us the coordinates of any given
feature on a older assembly.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div><font style="background-color:rgb(255,255,255)"
color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)"
color="#999999"> <a moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<div class="gmail_quote">On Tue, Oct 7, 2014 at 8:53 AM, Andy
Yates <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:ayates@ebi.ac.uk" target="_blank">ayates@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Duarte,<br>
<br>
You can access GRCh37 from <a moz-do-not-send="true"
href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>
port number 3337. Ensembl databases currently only hold the
contigs and assembly for a single assembly. That's why when
you try to get sequence for GRCh37 in the GRCh38 database
you get N's back<br>
<br>
Hope this helps,<br>
<br>
Andy<br>
<br>
------------<br>
Andrew Yates - Ensembl Support Coordinator<br>
European Molecular Biology Laboratory<br>
European Bioinformatics Institute<br>
Wellcome Trust Genome Campus<br>
Hinxton, Cambridge<br>
CB10 1SD, United Kingdom<br>
Tel: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-492538" value="+441223492538">+44-(0)1223-492538</a><br>
Fax: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-494468" value="+441223494468">+44-(0)1223-494468</a><br>
Skype: andrewyatz<br>
<a moz-do-not-send="true" href="http://www.ensembl.org/"
target="_blank">http://www.ensembl.org/</a><br>
<div>
<div class="h5"><br>
On 6 Oct 2014, at 17:23, Duarte Molha <<a
moz-do-not-send="true"
href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>>
wrote:<br>
<br>
> Dear developers<br>
><br>
> I have the latest API downloaded and I would want
to create a scritp that could retrieve sequence
information from a specified assembly<br>
><br>
> so I have made a script that tries to accomplish
this:<br>
><br>
> so ...assuming this coordinates:<br>
><br>
> chr: 5<br>
> from: 112043202<br>
> to: 112046226<br>
> strand = 1<br>
> assembly = GRCh38<br>
><br>
> my $slice = $slice_adaptor->fetch_by_region(
'chromosome', $chrom, $from, $to, $strand, $assembly );<br>
><br>
><br>
> $seq = $slice->seq();<br>
><br>
> I can retrieve the dna sequence:<br>
><br>
> >CHR5-112043202-112046226
chr5:112043202-112046226<br>
> AGTATATAATCACAT..............CTAAAAGCAAACA<br>
><br>
><br>
> However, if I give it the variables:<br>
><br>
> chr: 5<br>
> from: 112043202<br>
> to: 112046226<br>
> strand = 1<br>
> assembly = GRCh37 or NCBI36<br>
><br>
> i get :<br>
><br>
> >CHR5-112043202-112046226
chr5:112043202-112046226<br>
> NNNNNNNNN.........NNNNNNNNNNNNNNNN<br>
><br>
><br>
> How can I get the correct underlying sequence?<br>
><br>
> Best regards<br>
><br>
> Duarte<br>
</div>
</div>
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