Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.config
Class EnsemblComparaDivision
java.lang.Object
uk.ac.roslin.ensembl.config.EnsemblType
uk.ac.roslin.ensembl.config.EnsemblComparaDivision
- All Implemented Interfaces:
- Serializable, Comparable<EnsemblComparaDivision>, DatabaseType, ObjectType
public class EnsemblComparaDivision
- extends EnsemblType
- implements DatabaseType, Comparable<EnsemblComparaDivision>
In 'ensembl.org' there is a single 'ensembl_compara' database which contains
the pairwise comparison data on all the species in 'ensembl.org. However, in
'ensemblgenomes.org', there are separate 'ensembl_compara' databases for the
different taxonomic groupings:
- ensembl_compara_plants
- ensembl_compara_bacteria
- ensembl_compara_fungi
- ensembl_compara_metazoa
- ensembl_compara_protozoa
- ensembl_compara_pan_homology
In ensembl.org all species are compared in the ensembl_compara database, and
belong to the compara group 'multi'. In each core database (species) in
ensemblgenomes.org the 'species.division' key in table 'meta' specifies the
group:
- EnsemblPlants
- EnsemblBacteria
- EnsemblFungi
- EnsemblMetazoa
- EnsemblProtozoa
Orthology / paralogy (peptide) predictions are done between all species of a database,
but genomic alignments only between certain combinations of species. Bacteria
is a slightly special case in that we compare members of each collection to
each other, but not between the collections (its actually 10 comparas merged
into one).
ensembl_compara_pan_homology is a peptide compara database produced from
a set of selected species that are taken from all EnsemblGenomes divisions and
from Ensembl (but doesn't include all species from all divisions). See list at
http://metazoa.ensembl.org/info/docs/compara/homology_method.html.
One thing to note here is that pan also contains protein family data as well:
http://metazoa.ensembl.org/info/docs/compara/family.html. This means that
the genome_db table ends up with more entries than are used in the peptide
homology comparisons alone and cannot be used to determine membership, so you
need to use the species_set/method_link tables as well rather than just relying
on genome_db.
- See Also:
- Serialized Form
MULTI
public static EnsemblComparaDivision MULTI
PLANTS
public static EnsemblComparaDivision PLANTS
PROTISTS
public static EnsemblComparaDivision PROTISTS
BACTERIA
public static EnsemblComparaDivision BACTERIA
FUNGI
public static EnsemblComparaDivision FUNGI
METAZOA
public static EnsemblComparaDivision METAZOA
PAN_HOMOLOGY
public static EnsemblComparaDivision PAN_HOMOLOGY
getDBName
public static String getDBName(String label)
getAllTypes
public static Collection<EnsemblComparaDivision> getAllTypes()
getEnsemblComparaDivision
public static EnsemblComparaDivision getEnsemblComparaDivision(String value)
getEnsemblComparaDivisionByMetaValue
public static EnsemblComparaDivision getEnsemblComparaDivisionByMetaValue(String value)
compareTo
public int compareTo(EnsemblComparaDivision other)
- Specified by:
compareTo
in interface Comparable<EnsemblComparaDivision>
Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3