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

Field Summary

Fields

Modifier and Type	Field and Description
static EnsemblComparaDivision	BACTERIA
static EnsemblComparaDivision	FUNGI
static EnsemblComparaDivision	INCOMPLETE_SEARCH
static EnsemblComparaDivision	METAZOA
static EnsemblComparaDivision	MULTI
static EnsemblComparaDivision	PAN_HOMOLOGY
static EnsemblComparaDivision	PLANTS
static EnsemblComparaDivision	PROTISTS

Fields inherited from class uk.ac.roslin.ensembl.config.EnsemblType

label

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(EnsemblComparaDivision other)
static Collection<EnsemblComparaDivision>	getAllTypes()
static String	getDBName(String label)
static EnsemblComparaDivision	getEnsemblComparaDivision(String value)
static EnsemblComparaDivision	getEnsemblComparaDivisionByMetaValue(String value)

Methods inherited from class uk.ac.roslin.ensembl.config.EnsemblType

toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

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

INCOMPLETE_SEARCH

public static EnsemblComparaDivision INCOMPLETE_SEARCH

Method Detail

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>