[ensembl-dev] Multiple alignment for more than 2 species

[Dazong Zhou]

An ideal answer! Thank you, Matthieu.

Hunter

2014-09-10 16:56 GMT+08:00 Matthieu Muffato <muffato at ebi.ac.uk>:

> Dear Hunter,
>
> The code on the tutorial indeed only works for pairwise alignments, for
> which we use LastZ.
> We use a different method for the multiple alignments: EPO
> http://www.ensembl.org/info/genome/compara/analyses.html#epo
>
> You can refer to our workshop exercises (in docs/workshop/) for an example
> of how to load multiple alignments:
> https://github.com/Ensembl/ensembl-compara/blob/release/
> 76/docs/workshop/API_workshop_exercises/GenomicAlignBlock_2.pl
> But first replace
>   fetch_by_dbID("619");
> with
>   fetch_by_method_link_type_species_set_name("EPO", "mammals")
> 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
>
> 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.
>
> Hope this helps,
> Matthieu
>
>
> On 10/09/14 09:42, Dazong Zhou wrote:
>
>> Hi,
>>
>> I get problems on multiple sequence alignment for more than 2 species
>> using the sample code at:
>> http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html (the
>> code below "Here is an example script with all of this:").
>>
>> The sample runs well on default, but fails on adding additional species.
>> That is to say, the below code works when changing "human:mouse" to
>> "human:dog" but returns no data when changing to "human:mouse:dog" .
>>
>>
>> my $species = "human";
>> my $coord_system = "chromosome";
>> my $seq_region = "14";
>> my $seq_region_start = 75000000;
>> my $seq_region_end = 75010000;
>> my $alignment_type = "LASTZ_NET";
>> my $set_of_species = "human:mouse";
>> my $output_file = undef;
>> my $output_format = "clustalw";
>> my $help;
>>
>> GetOptions(
>>      "help" => \$help,
>>      "species=s" => \$species,
>>      "coord_system=s" => \$coord_system,
>>      "seq_region=s" => \$seq_region,
>>      "seq_region_start=i" => \$seq_region_start,
>>      "seq_region_end=i" => \$seq_region_end,
>>      "alignment_type=s" => \$alignment_type,
>>      "set_of_species=s" => \$set_of_species,
>>      "output_format=s" => \$output_format,
>>      "output_file=s" => \$output_file);
>>
>> Thanks,
>> Hunter
>>
>>
>>
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>>
> --
> Matthieu Muffato, Ph.D.
> Ensembl Compara 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
>
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