<div dir="ltr"><div><div><div>Hi, Stephen<br><br>Thank you very much for you help.<br><br></div>This solves my problem. So column 4 like Ggor-Hsap-Hsap-Pabe[4] stands for an ancestor of these listed species to which the base has been preserved.<br> <br></div>May I also know the script you used to get the tree and alignment info as seen in your email?<br></div><div><div><div><div><div class="gmail_extra"><br></div><div class="gmail_extra">I tried :<br></div><div class="gmail_extra"><p>"my $mlss = $mlss_adaptor->fetch_by_method_link_type_species_set_name("EPO", "mammals");</p><p>my $slice = $slice_adaptor->fetch_by_region('toplevel', $seq_region, $seq_region_start, $seq_region_end);</p>my $genomic_align_blocks =$genomic_align_block_adaptor ->fetch_all_by_<p>MethodLinkSpeciesSet_Slice($mlss, $slice); <br></p><p>" to fetch the ancestral sequences.</p><p>But it doesn't seem to work.<br></p>Thanks<br></div><div class="gmail_extra">Haiming<br><br></div><div class="gmail_extra"><div class="gmail_quote">On Mon, Sep 29, 2014 at 8:42 AM, Stephen Fitzgerald <span dir="ltr"><<a href="mailto:stephenf@ebi.ac.uk" target="_blank">stephenf@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Haiming, column 4 lists the set of species whose ancestor had the same base as human (we use a program called Ortheus to infer the sequence of the ancestral nodes in the tree connecting all the extant species).<br>
<br>
For example:<br>
<br>
chr1 1031796 1031797 Mmul-Panu-Hsap-Ptro[4] 196 50,50,255<br>
<br>
The ancestral sequence of the primates present in the alignment at this position in human (maked with a "*") is the most recent common ancestor to share a G base with human (this is at the root of the 4 primates in the alignment). The next deepest ancestor (between rodents and primates, marked with a "**") is predicted to have a T at this position. So, somewhere between these two ancestors the base changed T->G. Hence, this position would be marked as primate specific.<br>
<br>
<br>
Human › chromosome:GRCh38:1:1031796:<u></u>1031797:1<br>
Ancestral sequences › (homo_sapiens,pan_troglodytes)<u></u>;<br>
Chimpanzee › chromosome:CHIMP2.1.4:7:<u></u>159477370:159477371:1<br>
Ancestral sequences › ((homo_sapiens,pan_<u></u>troglodytes),(papio_anubis,<u></u>macaca_mulatta)); *<br>
Macaque › chromosome:MMUL_1:1:4106934:<u></u>4106935:1<br>
Ancestral sequences › (papio_anubis,macaca_mulatta);<br>
Olive baboon › scaffold:PapAnu2.0:JH684932.1:<u></u>192067:192068:1<br>
Ancestral sequences › (((homo_sapiens,pan_<u></u>troglodytes),(papio_anubis,<u></u>macaca_mulatta)),(mus_<u></u>musculus,rattus_norvegicus)); **<br>
Mouse › chromosome:GRCm38:4:156188534:<u></u>156188535:-1<br>
Ancestral sequences › (mus_musculus,rattus_<u></u>norvegicus);<br>
Rat › chromosome:Rnor_5.0:5:<u></u>177087882:177087883:-1<br>
Ancestral sequences › ((((homo_sapiens,pan_<u></u>troglodytes),(papio_anubis,<u></u>macaca_mulatta)),(mus_<u></u>musculus,rattus_norvegicus)),(<u></u>(sus_scrofa,bos_taurus),canis_<u></u>familiaris));<br>
Cow › chromosome:UMD3.1:16:52694475:<u></u>52694476:-1<br>
Ancestral sequences › (sus_scrofa,bos_taurus);<br>
Pig › chromosome:Sscrofa10.2:6:<u></u>57872690:57872691:-1<br>
Ancestral sequences › ((sus_scrofa,bos_taurus),<u></u>canis_familiaris);<br>
Dog › chromosome:CanFam3.1:5:<u></u>56250642:56250643:1<br>
<br>
<br>
Human G<br>
Ancestral sequences G<br>
Chimpanzee G<br>
Ancestral sequences G *<br>
Macaque G<br>
Ancestral sequences G<br>
Olive baboon G<br>
Ancestral sequences T **<br>
Mouse C<br>
Ancestral sequences C<br>
Rat C<br>
Ancestral sequences T<br>
Cow T<br>
Ancestral sequences T<br>
Pig G<br>
Ancestral sequences T<br>
Dog T<br>
<br>
<br>
We don't store speciation times for the age of base track. Information regarding speciation times can be obtained from sites such as Time Tree (<a href="http://www.timetree.org/" target="_blank">http://www.timetree.org/</a>).<br>
<br>
HTH,<br>
Stephen.<br>
<br>
On Fri, 26 Sep 2014, Tang, Haiming wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
HI, Stephen<br>
I followed your instructions and got the bed file.<br>
<br>
Column 4 appears to list the species for which that base is the same as in human, since it looks like Hsap is in every line. <br>
The number in square brackets [] is just the number of species listed.<br>
<br>
But the file doesn’t seem to give the age of the base. <br>
<br>
For example: How to interpret Ggor-Hsap-Hsap-Pabe[4] in <br>
<br>
"chrY 57107125 57107126 Ggor-Hsap-Hsap-Pabe[4] 120 30,30,255"?<br>
<br>
Are Ggor and Hsap ancestral species? <br>
<br>
Or Age of base is stored at somewhere else?<br>
<br>
Thanks<br>
<br>
Haiming<br>
<br>
On Fri, Sep 26, 2014 at 2:47 AM, Stephen Fitzgerald <<a href="mailto:stephenf@ebi.ac.uk" target="_blank">stephenf@ebi.ac.uk</a>> wrote:<br>
Hi Haiming,<br>
the compara API is used to retrieve information from the compara database. However the "Age of Base" track is<br>
generated from a Bigbed binary file, so it is not part of the compara database. The Bigbed file is generated from a<br>
Bed file. I have transferred this Bed file (from release 76) to our ftp site. You can retrieve this file using<br>
anonymous ftp from here:<br>
<br>
ftp <a href="http://ftp.ebi.ac.uk" target="_blank">ftp.ebi.ac.uk</a><br>
<br>
cd pub/software/ensembl/stephen/<u></u>BaseAge/<br>
<br>
get base_age_76.bed.gz<br>
<br>
Hope this helps,<br>
Stephen.<br>
<br>
<br>
On Thu, 25 Sep 2014, Tang, Haiming wrote:<br>
<br>
<br>
DEAR GROUP, MY NAME IS HAIMING TANG. I'M IN DR PAUL THOMAS'S GROUP IN UNIVERSITY OF SOUTHERN<br>
CALIFORNIA.<br>
<br>
I'm trying to retrieve "Age of Base" using Perl API.<br>
<br>
As described in "<a href="http://www.ensembl.org/info/genome/compara/analyses.html#age_of_base" target="_blank">http://www.ensembl.org/info/<u></u>genome/compara/analyses.html#<u></u>age_of_base</a>"<br>
<br>
"Age of Base<br>
<br>
From these ancestral sequences, we infer the age of a base, i.e. the timing of the most recent mutation<br>
for each<br>
base of the genome. Each position of the human genome is compared to its immediate inferred ancestor,<br>
then its<br>
ancestor, etc. until a difference is found. The inferred substitution event therefore occurred on a<br>
specific<br>
branch of the tree, which is identified by all the extant species which eventually descended from that<br>
branch, as<br>
illustrated below."<br>
<br>
"Age of base" has close relation with EPO ancestral alignment. But I could find any related method in<br>
Compara Perl<br>
API Documentation or Compara API Tutorial.<br>
<br>
Can anyone show me how to do to retrieve "age of base"?<br>
<br>
Thank you in advance.<br>
<br>
Haiming<br>
<br>
<br>
<br>
<br>
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</blockquote>
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