<div dir="ltr"><div>An ideal answer! Thank you, <span style="font-family:arial,sans-serif;font-size:14px">Matthieu.</span></div><div><span style="font-family:arial,sans-serif;font-size:14px"><br></span></div>Hunter</div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-10 16:56 GMT+08:00 Matthieu Muffato <span dir="ltr"><<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Hunter,<br>
<br>
The code on the tutorial indeed only works for pairwise alignments, for which we use LastZ.<br>
We use a different method for the multiple alignments: EPO <a href="http://www.ensembl.org/info/genome/compara/analyses.html#epo" target="_blank">http://www.ensembl.org/info/<u></u>genome/compara/analyses.html#<u></u>epo</a><br>
<br>
You can refer to our workshop exercises (in docs/workshop/) for an example of how to load multiple alignments:<br>
<a href="https://github.com/Ensembl/ensembl-compara/blob/release/76/docs/workshop/API_workshop_exercises/GenomicAlignBlock_2.pl" target="_blank">https://github.com/Ensembl/<u></u>ensembl-compara/blob/release/<u></u>76/docs/workshop/API_workshop_<u></u>exercises/GenomicAlignBlock_2.<u></u>pl</a><br>
But first replace<br>
fetch_by_dbID("619");<br>
with<br>
fetch_by_method_link_type_<u></u>species_set_name("EPO", "mammals")<br>
The pair ("EPO", "mammals") can be found at the header of each table in the first link. You could use ("EPO", "primates") if you're only interested in primates, etc<br>
<br>
Note that multiple alignments can only be loaded as a whole (in this case: the 16 mammals): you can't ask for only 3 species in the set.<br>
<br>
Hope this helps,<br>
Matthieu<div><div class="h5"><br>
<br>
On 10/09/14 09:42, Dazong Zhou wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi,<br>
<br>
I get problems on multiple sequence alignment for more than 2 species<br>
using the sample code at:<br>
<a href="http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html" target="_blank">http://www.ensembl.org/info/<u></u>docs/api/compara/compara_<u></u>tutorial.html</a> (the<br>
code below "Here is an example script with all of this:").<br>
<br>
The sample runs well on default, but fails on adding additional species.<br>
That is to say, the below code works when changing "human:mouse" to<br>
"human:dog" but returns no data when changing to "human:mouse:dog" .<br>
<br>
<br>
my $species = "human";<br>
my $coord_system = "chromosome";<br>
my $seq_region = "14";<br>
my $seq_region_start = 75000000;<br>
my $seq_region_end = 75010000;<br>
my $alignment_type = "LASTZ_NET";<br>
my $set_of_species = "human:mouse";<br>
my $output_file = undef;<br>
my $output_format = "clustalw";<br>
my $help;<br>
<br>
GetOptions(<br>
"help" => \$help,<br>
"species=s" => \$species,<br>
"coord_system=s" => \$coord_system,<br>
"seq_region=s" => \$seq_region,<br>
"seq_region_start=i" => \$seq_region_start,<br>
"seq_region_end=i" => \$seq_region_end,<br>
"alignment_type=s" => \$alignment_type,<br>
"set_of_species=s" => \$set_of_species,<br>
"output_format=s" => \$output_format,<br>
"output_file=s" => \$output_file);<br>
<br>
Thanks,<br>
Hunter<br>
<br>
<br>
<br></div></div>
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</blockquote>
<br>
-- <br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara 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>
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