Changes for version 113.0.0 - 2024-10-17 (TRIAL RELEASE)
- Release for Ensembl 113
Changes for version 113.0.0 - 2024-10-18
Modules
API to connect to and work with EnsEMBL genomic databases
Stores details of an analysis run
Dna pairwise alignment module
A feature that represents an assembly exception
Handles mapping between two coordinate systems using the information stored in the assembly table.
A generic Attribute class.
Baseclass providing a common abstract implmentation for alignment features
Object representing a CDS
Arbitary Slice of a genome
Run time database loader
Adaptor for the manipulation of Alternative allele groupings
adaptor/factory for MappedSlices representing alternative assemblies
Provides database interaction for Bio::EnsEMBL::Attribute objects.
Base Adaptor for DBSQL adaptors
Abstract Base class for AlignFeatureAdaptors
An Abstract Base class for all FeatureAdaptors
Encapsulates all generic access to database meta information
An adaptor which performs database interaction relating to the storage and retrieval of Biotypes
Adaptor for DnaAlignFeatures
An adaptor responsible for the retrieval and storage of exon objects
Database adaptor for the retrieval and storage of Gene objects
Encapsulates all access to core database meta information
Provides database interaction for Bio::EnsEMBL::MiscSet objects.
Database adaptor for the retrieval and storage of Operon objects
Database adaptor for the retrieval and storage of OperonTranscript objects
Performs database interaction for PredictionExons.
Adaptor for ProteinAlignFeatures
Database connection wrapper allowing for one backing connection to be used for multiple DBs
Provides a means to fetch and store RNAProduct objects from a database.
produce sequence strings from locations
A database aware adaptor responsible for the creation of Slice objects.
Base cache code
ID based caching using all available values
ID based caching using an LRU backed cache
Retrieves supporting features from the database.
An adaptor which performs database interaction relating to the storage and retrieval of Transcripts
Retrieves supporting features from the database.
Provides a means to fetch and store Translation objects from a database.
A feature representing a density, or precentage coverage etc. in a given region.
A type representing a density, or percentage coverage etc. in a given region.
Ensembl specific dna-dna pairwise alignment feature
Ensembl specific dna-pep pairwise alignment feature
A class representing an Exon
An Exon feature in relation to a transcript
Ensembl specific sequence feature.
Stores sequence Features which are themselves hits to other sequence features.
Object representing a genes
A generic Genome class.
create gene_archive and peptide_archive
base object for IdMapping objects
a cache to hold data objects used by the IdMapping application
object representing a ScoredMappingMatrix entry
default Ensembl InternalIdMapper implementation for genes
object holding a list of Entries
analyse stable Id mapping results
score builder base class
object holding a list of scored Entries
base class for serialisable objects
default Ensembl StableIdGenerator implementation
framework representing syntenic regions across the genome
object representing syntenic regions
lightweight exon object
lightweight feature object
lightweight gene object
lightweight transcript object
lightweight translation object
A class representing an Intron
Arbitary Slice of a genome
Object representing a MANE transcript
an object representing a mapped slice
container for mapped slices
One side of a map pair
A class representing a microRNA product of a transcript
A miscelaneous feature with arbitrary features and associations.
This is a set representing a classification of a group of miscellaneuos features.
Object representing an operon
Object representing a polycistronic transcript that is part of an operon
Ensembl specific pep-dna pairwise alignment feature
A class representing an Exon from an ab initio prediction method
part of the list that is returned from project function calls
A class representing the mature RNA product of a transcript
A feature representing a repeat on a piece of sequence.
Arbitary Slice of a genome
A class representing a post transcriptional edit to a sequence.
Ensembl specific sequence feature.
A simple feature with a location and label
Arbitary Slice of a genome
object representing a stable ID history tree
Object representing a stop codon readthrough edit in a sequence
object representing an Ensembl transcript
Module having the fset2transcript* subroutines
A utility class used to perform coordinate conversions between a number of coordinate systems relating to transcripts
A class representing the translation of a transcript
A UTR feature with a location and a type (five prime/3 prime)
A object representing why a particular entity was NOT mapped to the ensembl.
Object that defines an upstream region
Utility functions for argument handling
bitstring object implementation
LRU Cache in Memory
configuration parser for perl scripts
Utility module for Vega release and schema conversion scripts
the instance converter
Bespoke Ensembl profiler
DESCRIPTION of Object
Utility functions for error handling
Utility module for Vega release and schema conversion scripts
Utility class for mapping between RNA-product types used in the Ensembl database and respective Perl API classes.
Utility module for Vega schema conversion script
A shared LRU cache of information about seq_regions
Utility functions for sequences
Utility functions for slices
Finds canonical transcripts
Provides
in lib/Bio/EnsEMBL/DBSQL/Driver.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/Oracle.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/Pg.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/SQLite.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/Sybase.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/TestDummy.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/mysql.pm
in lib/Bio/EnsEMBL/DBSQL/Driver/odbc.pm
in lib/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
in lib/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
in lib/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm
in lib/Bio/EnsEMBL/DataFile.pm
in lib/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
in lib/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
in lib/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
in lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
in lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
in lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
in lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/AedesAegypti.pm
in lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
in lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/PristionchusPacificus.pm
in lib/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
in lib/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
in lib/Bio/EnsEMBL/Utils/CigarString.pm
in lib/Bio/EnsEMBL/Utils/ConfigRegistry.pm
in lib/Bio/EnsEMBL/Utils/Converter.pm
in lib/Bio/EnsEMBL/Utils/Converter/bio_ens_analysis.pm
in lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
in lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hsp.pm
in lib/Bio/EnsEMBL/Utils/Scalar.pm
in lib/Bio/EnsEMBL/Utils/ScriptUtils.pm
in lib/Bio/EnsEMBL/Utils/VegaCuration/Gene.pm
in lib/Bio/EnsEMBL/Utils/VegaCuration/Transcript.pm
in lib/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm