<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div></div></div><div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin: 0px; "><b>From: </b><a href="mailto:mp@ebi.ac.uk">mp@ebi.ac.uk</a><br></div><div style="margin: 0px; "><b>Subject: </b><b>Re: Inquiry: Cafe.v3 Input</b><br></div><div style="margin: 0px; "><b>Date: </b>July 27, 2013 9:28:02 AM CDT<br></div><div style="margin: 0px; "><b>To: </b>"Mike Montague" <<a href="mailto:mmontagu@genome.wustl.edu">mmontagu@genome.wustl.edu</a>><br></div><div style="margin: 0px; "><b>Cc: </b><a href="mailto:mp@ebi.ac.uk">mp@ebi.ac.uk</a>, "Wes Warren" <<a href="mailto:wwarren@genome.wustl.edu">wwarren@genome.wustl.edu</a>></div></blockquote></div><div><br></div><div><blockquote type="cite">Dear Mike,<br><br>I am out of the office for some weeks with very limited access to the<br>internet at the moment. Looking at your error, it looks like the problem<br>is trying to connect with the DB or a general ensembl API problem. I don't<br>have at hand the script, but if you can send the interesting parts to<br><a href="mailto:ensembl-dev@ebi.ac.uk">ensembl-dev@ebi.ac.uk</a> you may be able to find a useful answer in short<br>time.<br>I will take a look as soon as I can once I am back.<br><br>Cheers,<br><br>M;</blockquote></div><div></div><blockquote type="cite"><div><br></div><div><br></div><div><div style="margin: 0px; "><b>From: </b>Wes Warren <<a href="mailto:wwarren@genome.wustl.edu">wwarren@genome.wustl.edu</a>><br></div><div style="margin: 0px; "><b>Subject: </b><b>Fwd: Re: Fwd: dN/dS</b><br></div><div style="margin: 0px; "><b>Date: </b>July 9, 2013 1:48:47 PM CDT<br></div><div style="margin: 0px; "><b>To: </b>Mike Montague <<a href="mailto:mmontagu@genome.wustl.edu">mmontagu@genome.wustl.edu</a>><br></div><br><div bgcolor="#FFFFFF" text="#000000">Mike,<br><br>The scripts you will need to retrieve cat data for cafe3. For cafe3 you need 1) a data file containing<br>gene family sizes for the taxa included in the tree and 2) a Newick formatted tree, including branch lengths for each gene family. <br><br>Wes<br><br>-------- Original Message -------<div class="moz-forward-container"><table class="moz-email-headers-table" border="0" cellpadding="0" cellspacing="0" style="position: static; z-index: auto; "><tbody><tr><th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:</th><td>Re: Fwd: dN/dS</td></tr><tr><th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date:</th><td>Fri, 08 Mar 2013 17:24:06 +0000</td></tr><tr><th align="RIGHT" nowrap="nowrap" valign="BASELINE">From:</th><td>Miguel Pignatelli <a class="moz-txt-link-rfc2396E" href="mailto:mp@ebi.ac.uk"><mp@ebi.ac.uk></a></td></tr><tr><th align="RIGHT" nowrap="nowrap" valign="BASELINE">To:</th><td>Wes Warren <a class="moz-txt-link-rfc2396E" href="mailto:wwarren@genome.wustl.edu"><wwarren@genome.wustl.edu></a></td></tr><tr><th align="RIGHT" nowrap="nowrap" valign="BASELINE">CC:</th><td>Javier Herrero <a class="moz-txt-link-rfc2396E" href="mailto:jherrero@ebi.ac.uk"><jherrero@ebi.ac.uk></a>, Matthieu Muffato <a class="moz-txt-link-rfc2396E" href="mailto:muffato@ebi.ac.uk"><muffato@ebi.ac.uk></a></td></tr></tbody></table><br><br><pre>Hi Wes,
The CAFE data is stored in the compara database and is accessible via
the compara API.
I am sending you a file with the 43 genes expanded in cat with respect
to the carnivora taxon.
The columns in the file are:
gene_tree_root_id, gene names, number of members in cat, number of
members in the parent (carnivora), newick format of the species tree.
A couple of comments about this data:
- The newick tree contains the species names and the taxon_ids for the
internal nodes. The numbers are the number of members for each taxon.
- I have only considered significant expansions as reported by our CAFE
analysis. It would be possible to include genes in the "grey" zone (i.e.
genes with more members in cat vs carnivora, but the change not being
significant).
I am also sending you the script I have written to retrieve the data. It
accepts a taxon_id as input. I called it as follows:
$ perl get_expansions.pl 9685 > cat_expansions.txt
If you run the script with other taxon_ids, be aware that it also
reports genes for which the lowest common ancestor is the taxon_id of
interest (i.e. births at the taxon_id of interest).
Let me know if you have any doubt or need further help in getting the
data you want.
Cheers,
M;
On 07/03/13 20:15, Wes Warren wrote:
> Hi Miguel,
>
> Is this data available for cat? All the gene trees are available so I
> assume so but I am not sure where to find the CAFE files.
>
> Thanks,
> Wes
>
> On 3/7/13 12:15 PM, Javier Herrero wrote:
>> Hi Wes
>>
>> This is a question for Miguel, our CAFE expert.
>>
>> Javier
>>
>> On 06/03/13 17:00, Wes Warren wrote:
>>> Is the CAFE output available for cat? We are interested in gene
>>> expansion outliers for the cat lineage, perhaps correlating these
>>> with carnivora.
>>>
>>> Wes
>>></pre></div></div></div></blockquote><div><br></div></div></div><br></body></html>