Maximilian Haeussler wrote:
Hi,
I have discovered a little inconsistency in biomart.
Usually, the orthologs between two species are stored in a mart called
compara_speciesx_speciesy_orthologs, where speciesx and speciesy are
sorted alphabetically.
Hi,
I've checked it - the species are indeed sorted alphabetically. In my
pipeline full names are used, sorted (as a convention), and then at some
stage trimmed to create the table names.
In the case of droso and zebrafish you have :
X = Danio
Y = Drosophila
so it's normal to see
drer__dmel
If you script this, I would advice to get the full species names from
the genome_db table in ensembl_compara database.
([EMAIL PROTECTED]) [ensembl_compara_42]> select name,
assembly from genome_db where name like "Danio%" OR name like "Droso%" ;
+-------------------------+----------+
| name | assembly |
+-------------------------+----------+
| Danio rerio | ZFISH6 |
| Drosophila melanogaster | BDGP4.3 |
+-------------------------+----------+
Benoit
--
Benoit Ballester, PhD
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom
