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<p>Hi Jinrui,</p>
<p>To configure the Registry on human GRCh38 (i.e. the default
Ensembl database), use<br>
</p>
<pre>Bio::EnsEMBL::Registry->load_registry_from_url('<a class="moz-txt-link-abbreviated" href="mailto:mysql://anonymous@ensembldb.ensembl.org">mysql://anonymous@ensembldb.ensembl.org</a>');
</pre>
<p>And for GRCh37:</p>
<pre>Bio::EnsEMBL::Registry->load_registry_from_url('<a class="moz-txt-link-abbreviated" href="mailto:mysql://anonymous@ensembldb.ensembl.org:3337">mysql://anonymous@ensembldb.ensembl.org:3337</a>');</pre>
<p>You can either directly call this in your script, or put it in a
registry configuration file named "configuration_file" since you
are calling $registry->load_all("configuration_file");<br>
</p>
<p>There is more documentation about using and setting up the
Registry at <a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/registry.html">http://www.ensembl.org/info/docs/api/registry.html</a><br>
</p>
<p>Hope this helps,<br>
Mattthieu<br>
</p>
<div class="moz-cite-prefix">On 24/03/2019 16:04, Jin-Rui Xu wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAFZUdz7y9dWgh4D7Rdpjnt2cxXB2equkkAWmwwLyifPwJ=RR5A@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Matthieu,
<div><br>
</div>
<div>The script you provided helps a lot!</div>
<div>For a genomic region in human, I need its alignment in
another species. Therefore, I need to know the species names.
Here is the short script, but it returns no names. My question
is how to find the species names used by the compara API?
Another question is about the genomic version, I think by
default the perl API uses human genome 38, but how to use 37
with the API?</div>
<div>Many thanks!</div>
<div>Jinrui</div>
<div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures;color:rgb(208,59,255)">use</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"> </span><span
class="gmail-s3"
style="font-variant-ligatures:no-common-ligatures;color:rgb(52,161,161)">Bio</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures">::EnsEMBL::Registry;</span></p>
<p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:11px"><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="gmail-p3"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(175,55,130)"><span
class="gmail-s4"
style="font-variant-ligatures:no-common-ligatures;color:rgb(52,163,39)">my</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">
$</span><span class="gmail-s6"
style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">registry</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">
= </span><span class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures">'Bio::EnsEMBL::Registry'</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">;</span></p>
<p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:11px"><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="gmail-p3"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(175,55,130)"><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">$</span><span
class="gmail-s6"
style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">registry</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">->load_all(</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures">"configuration_file"</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">);</span></p>
<p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:11px"><span
style="font-variant-ligatures:no-common-ligatures;color:rgb(215,57,30)">
</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s4"
style="font-variant-ligatures:no-common-ligatures;color:rgb(52,163,39)">my</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"> @</span><span
class="gmail-s7"
style="text-decoration-line:underline;font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">species_names</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"> = @{$</span><span
class="gmail-s6"
style="font-variant-ligatures:no-common-ligatures;color:rgb(205,121,35)">registry</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures">->get_all_species()
};</span></p>
<p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:11px"><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="gmail-p3"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(175,55,130)"><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">print
</span><span class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures">"@species_names\n"</span><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">;</span></p>
<p class="gmail-p3"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo;color:rgb(175,55,130)"><span
class="gmail-s5"
style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"><br>
</span></p>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Mar 20, 2019 at 1:58
PM Matthieu Muffato <<a href="mailto:muffato@ebi.ac.uk"
moz-do-not-send="true">muffato@ebi.ac.uk</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi Jinrui</p>
<p>Have a look back at my first email. There is an example
URL to our REST API server to get the alignment of a human
region</p>
<p>If you want to use the Perl API, you can adapt
<a
class="gmail-m_8876899558341469702moz-txt-link-freetext"
href="https://github.com/Ensembl/ensembl-presentation/blob/master/API/Compara/exercises/gab1.pl"
target="_blank" moz-do-not-send="true">https://github.com/Ensembl/ensembl-presentation/blob/master/API/Compara/exercises/gab1.pl</a><br>
</p>
<p>Regards,<br>
Matthieu<br>
</p>
<div class="gmail-m_8876899558341469702moz-cite-prefix">On
18/03/2019 16:53, Jin-Rui Xu wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Matthieu,
<div><br>
</div>
<div>I am going to use the human self-alignment to
detect paralogous genomic regions (particularly non
coding regions). But I can not find examples of API
for this purpose. Could you pass me some scripts or
examples where I can start? Say I have a human genomic
coordinate, and want to find its paralogous regions
and alignments.</div>
<div>Many thanks.</div>
<div>Jinrui</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Mar 13, 2019
at 8:37 AM Matthieu Muffato <<a
href="mailto:muffato@ebi.ac.uk" target="_blank"
moz-do-not-send="true">muffato@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi Jinrui</p>
<p>In all our pairwise alignments, we refine the
LastZ alignment blocks with two steps called
"chaining" and "netting" (see <a
class="gmail-m_8876899558341469702gmail-m_-1501946497467315318moz-txt-link-freetext"
href="http://europepmc.org/articles/PMC4852398"
target="_blank" moz-do-not-send="true">http://europepmc.org/articles/PMC4852398</a>
and <a
class="gmail-m_8876899558341469702gmail-m_-1501946497467315318moz-txt-link-freetext"
href="http://genomewiki.ucsc.edu/index.php/Chains_Nets" target="_blank"
moz-do-not-send="true">http://genomewiki.ucsc.edu/index.php/Chains_Nets</a>
for more information). What you get in our
database is the product of these two steps.<br>
The netting phase is done on the reference species
only, we don't do bidirectional netting. This
means that there is very little overlap / nesting
on the reference species (human in the case of the
human vs * alignments). Overlap / nesting is
allowed on the non-reference species, though. For
instance, in the human-mouse alignments, there are
20,000 pairs of blocks that overlap on human, and
1,900,000 pairs of blocks that overlap on mouse.<br>
</p>
<p>So in this case, yes you can identify human
paralogous regions 1) through the self-alignment
and 2) through the human-mouse alignment (or any
pairwise alignment that involves human) by finding
human regions that align to the same region in the
other species</p>
<p>Hope this helps,</p>
<p>Matthieu<br>
</p>
<div
class="gmail-m_8876899558341469702gmail-m_-1501946497467315318moz-cite-prefix">On
11/03/2019 19:45, Jin-Rui Xu wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Matthieu,</div>
<div><br>
</div>
<div>Thank you very much for your email. </div>
<div><br>
</div>
<div>I am wondering in the human self alignment,
one genomic region may be mapped to multiple
other regions. These multiple hits also exist
in e.g. human vs mouse genome alignment.</div>
<div>Does ensembl provide all these multiple
regions or just the best one? Can these
multiple hits achieved by compara perl API?</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Jinrui</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
<div><br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Mar
11, 2019 at 3:05 PM Matthieu Muffato <<a
href="mailto:muffato@ebi.ac.uk"
target="_blank" moz-do-not-send="true">muffato@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Dear
Jinrui,<br>
<br>
We have a human self-alignment, that has
been computed with LastZ and <br>
identifies paralogous regions within the
genome. You can find the whole <br>
alignment on the FTP <br>
<a
href="ftp://ftp.ensembl.org/pub/current_maf/ensembl-compara/pairwise_alignments/"
rel="noreferrer" target="_blank"
moz-do-not-send="true">ftp://ftp.ensembl.org/pub/current_maf/ensembl-compara/pairwise_alignments/</a>
<br>
but also query specific regions: <br>
<a
href="http://rest.ensembl.org/alignment/region/homo_sapiens/17:63997797-64000390:1?species_set=homo_sapiens;content-type=application/json;method=LASTZ_NET"
rel="noreferrer" target="_blank"
moz-do-not-send="true">http://rest.ensembl.org/alignment/region/homo_sapiens/17:63997797-64000390:1?species_set=homo_sapiens;content-type=application/json;method=LASTZ_NET</a><br>
<br>
Human is the only species for which we have
a self-alignment.<br>
<br>
Kind regards,<br>
Matthieu<br>
<br>
On 09/03/2019 03:10, Jin-Rui Xu wrote:<br>
> Hello,<br>
><br>
> I just started learning the compara
API. However, I am still not sure <br>
> whether it can address my questions. I
am wondering if someone could <br>
> give me some guidance and example
scripts. Here is my question: (1) I <br>
> want to identify all paralogous DNA
fragments (not neccessarily genes) <br>
> in a genome. One genomic regions may
have more than one duplicate. (2) <br>
> Then, I want to find in which of the
other species, the two paralogous <br>
> DNAs have a common ancestor.<br>
> Alternatively, I can focus on two
genomic regions in a genome to test <br>
> if they are paralogous, and then which
species has their common <br>
> ancestral DNA<br>
> How could I get this done using compara
API (version 95)?<br>
><br>
> Many thanks!<br>
><br>
> Jinrui<br>
<br>
-- <br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br>
Phone + 44 (0) 1223 49 4631<br>
Fax + 44 (0) 1223 49 4468<br>
<br>
</blockquote>
</div>
</div>
</blockquote>
<pre class="gmail-m_8876899558341469702gmail-m_-1501946497467315318moz-signature" cols="72">--
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468</pre>
</div>
</blockquote>
</div>
</blockquote>
<pre class="gmail-m_8876899558341469702moz-signature" cols="72">--
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468</pre>
</div>
</blockquote>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468</pre>
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