| AffyArray | A module to represent an Affymetrix array. |
| AffyFeature | A module to represent an Affy probe's genomic mapping. |
| AffyProbe | A module to represent an Affymetrix probe. |
| AlignStrainSlice | Represents the slice of the genome aligned with certain strains (applying the variations/indels) |
| Analysis | Stores details of an analysis run |
| ArchiveStableId | Bio::EnsEMBL::ArchiveStableId |
| AssemblyExceptionFeature | A feature that represents an assembly exception |
| AssemblyMapper | Handles mapping between two coordinate systems using the information stored in the assembly table. |
| Attribute | A generic Attribute class. |
| BaseAlignFeature | Baseclass providing a common abstract implmentation for alignment features |
| ChainedAssemblyMapper | Handles mapping between two coordinate systems using the information stored in the assembly table |
| Collection | Abstract base class for feature collection classes. |
| CoordSystem | Bio::EnsEMBL::CoordSystem |
| DBEntry | Object representing an external reference (xref) |
| DBLoader | Run time database loader |
| DensityFeature | A feature representing a density, or precentage coverage etc. in a given region. |
| DensityFeatureSet | A feature representing a set of density features |
| DensityType | A type representing a density, or percentage coverage etc. in a given region. |
| DnaDnaAlignFeature | Ensembl specific dna-dna pairwise alignment feature |
| DnaPepAlignFeature | Ensembl specific dna-pep pairwise alignment feature |
| Exon | A class representing an Exon |
| Feature | Ensembl specific sequence feature. |
| FeaturePair | Stores sequence Features which are themselves hits to other sequence features. |
| Gene | Object representing a genes |
| GoXref | Bio::EnsEMBL::GoXref |
| IdentityXref | Bio::EnsEMBL::IdentityXref |
| IndividualSlice | SubClass of the Slice. Represents the slice of the genome for a certain individual (applying the alleles for this individual) |
| IndividualSliceFactory | |
| Intron | |
| KaryotypeBand | Bio::EnsEMBL::DBSQL::KaryotypeBand |
| MappedSlice | an object representing a mapped slice |
| MappedSliceContainer | container for mapped slices |
| Mapper | Bio::EnsEMBL::Mapper |
| MiscFeature | A miscelaneous feature with arbitrary features and associations. |
| MiscSet | This is a set representing a classification of a group of miscellaneuos features. |
| OligoArray | A module to represent an oligonucleotide microarray. |
| OligoFeature | A module to represent an oligonucleotide probe's genomic mapping. |
| OligoProbe | A module to represent an oligonucleotide probe. |
| OntologyTerm | Bio::EnsEMBL::OntologyTerm |
| PepDnaAlignFeature | Ensembl specific pep-dna pairwise alignment feature |
| PredictionExon | A class representing an Exon from an ab initio prediction method |
| PredictionTranscript | PredictionTranscript |
| ProjectionSegment | part of the list that is returned from project function calls |
| ProteinFeature | Bio::EnsEMBL::ProteinFeature |
| Registry | Bio::EnsEMBL::Registry |
| RepeatConsensus | |
| RepeatFeature | A feature representing a repeat on a piece of sequence. |
| RepeatMaskedSlice | Arbitary Slice of a genome |
| Root | Bio::EnsEMBL::Root |
| SNP | Bio::EnsEMBL::SNP |
| SeqEdit | A class representing a post transcriptional edit to a sequence. |
| SeqFeature | Ensembl specific sequence feature. |
| SeqFeatureI | Bio::EnsEMBL::SeqFeatureI |
| SimpleFeature | A simple feature with a location and label |
| Slice | Arbitary Slice of a genome |
| StableIdEvent | object representing a stable ID mapping event |
| StableIdHistoryTree | object representing a stable ID history tree |
| Storable | Bio::EnsEMBL::Storable |
| StrainSlice | SubClass of the Slice. Represents the slice of the genome for a certain strain (applying the variations) |
| TopLevelAssemblyMapper | Handles mapping between a given coordinate system and the toplevel pseudo coordinate system. |
| Transcript | object representing an Ensembl transcript |
| TranscriptFactory | Module having the fset2transcript* subroutines |
| TranscriptMapper | A utility class used to perform coordinate conversions between a number of coordinate systems relating to transcripts |
| Translation | A class representing the translation of a transcript |
| UnconventionalTranscriptAssociation | A class representing an some sort of unconventional association between a gene and a transcript. |
| UnmappedObject | A object representing why a particular entity was NOT mapped to the ensembl. |
| Upstream | Object that defines an upstream region |