[ensembl-dev] Extracting ancestral sequence from EPO alignments

[Wanbo Li]

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
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Then another question, if I could dump the EPO alignments later on, how should I extract ancestral sequence for cow?


Sincerely,

Wanbo