[ensembl-dev] Extracting ancestral sequence from EPO alignments

[Kathryn Beal]

Hi Wanbo,
It is currently not possible to dump a subset of species using this method. The set_of_species parameter is used to select which EPO alignment to choose (e.g. this can either be the complete set of  the13 species used for this alignment or a short cut "mammals"). You also need to define where to find the species databases (the --db parameter) and the species used for this seq_region (the --species parameter). Also, currently it is only possible to get the ancestral sequences in maf or emf format (the --format parameter).

eg
 perl ~/src/ensembl_main/ensembl-compara/scripts/dumps/DumpMultiAlign.pl --db mysql://anonymous@ensembldb:5306/71 --compara_url mysql://anonymous@ensembldb:5306/ensembl_compara_71 --seq_region 3 --seq_region_start 10000000 --seq_region_end 10004000 --alignment_type EPO --set_of_species mammals --species cow --restrict --output_file test.epo --output_format maf

We also have dumps of the EPO 13 way eutherian alignments in emf format on the public ftp site 
ftp://ftp.ensembl.org/pub/release-71/emf/ensembl-compara/epo_13_eutherian/

I hope that helps,
Cheers
Kathryn

Kathryn Beal, PhD
European Bioinformatics Institute  (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK 
Tel. +44 (0)1223 494458
www.ensembl.org

On 17 Jun 2013, at 12:40, Wanbo Li wrote:

> Dear all,
> 
> I am trying to figure out how to extract ancestral sequence for cow based on EPO alignments.
> 
> Firstly, I tried the following command to download the EPO alignments for four species "horse:dog:pig:cow".   I got errors listed below, I will be very glad if someone let me know what I am doing wrong here.
> 
> perl ./ensembl-compara/scripts/dumps/DumpMultiAlign.pl --compara_url mysql://anonymous@ensembldb:5306/ensembl_compara_71 --seq_region 3 --seq_region_start 2000 --seq_region_end 6000 --alignment_type EPO --set_of_species horse:dog:pig:cow  --restrict --output_file test.epo
> 
> Could not connect to database ensembl_compara_71 as user anonymous using [DBI:mysql:database=ensembl_compara_71;host=ensembldb;port=5306] as a locator:
> Unknown MySQL server host 'ensembldb' (1) at /home/wanbo/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 312.
> 
> -------------------- EXCEPTION --------------------
> MSG: No matches found for name 'equus_caballus' and assembly '--undef--'
> STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:136
> STACK Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::__ANON__ /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm:583
> STACK Bio::EnsEMBL::Utils::Exception::try /home/wanbo/src/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm:528
> STACK Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_registry_aliases /home/wanbo/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm:584
> STACK toplevel ./ensembl-compara/scripts/dumps/DumpMultiAlign.pl:425
> Date (localtime)    = Mon Jun 17 13:21:20 2013
> Ensembl API version = 71
> ---------------------------------------------------
> 
> 
> Then another question, if I could dump the EPO alignments later on, how should I extract ancestral sequence for cow?
> 
> 
> Sincerely,
> 
> Wanbo
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