Uses of Package
org.biojava3.core.sequence

Packages that use org.biojava3.core.sequence

org.biojava3.core.sequence
org.biojava3.core.sequence.io
org.biojava3.core.sequence.loader
org.biojava3.core.sequence.location
org.biojava3.core.sequence.location.template
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template
org.biojava3.core.sequence.transcription

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence

AccessionID
Used in Sequences as the unique indentifier.

CDSSequence
Represents a exon or coding sequence in a gene.

ChromosomeSequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences

DataSource
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier

DNASequence
This is class should model the attributes associated with a DNA sequence

DNASequence.DNAType
The type of DNA sequence

ExonSequence
A gene contains a collection of Exon sequences

GeneSequence

IntronSequence

ProteinSequence
The representation of a ProteinSequence

RNASequence
RNASequence where RNACompoundSet are the allowed values

SequenceOptimizationHints.SequenceCollection

SequenceOptimizationHints.SequenceUsage

StartCodonSequence
Used to map the start codon feature on a gene

StopCodonSequence
Used to map the stop codon sequence on a gene

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

TranscriptSequence
This is the sequence if you want to go from a gene sequence to a protein sequence.

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.io

DNASequence
This is class should model the attributes associated with a DNA sequence

GeneSequence

ProteinSequence
The representation of a ProteinSequence

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.loader

AccessionID
Used in Sequences as the unique indentifier.

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.location

AccessionID
Used in Sequences as the unique indentifier.

DataSource
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.location.template

AccessionID
Used in Sequences as the unique indentifier.

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.storage

AccessionID
Used in Sequences as the unique indentifier.

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.template

AccessionID
Used in Sequences as the unique indentifier.

Strand
Provides a way of representing the strand of a sequence, location hit or feature.

TaxonomyID
A sequence can be associated with a species or Taxonomy ID

Classes in org.biojava3.core.sequence used by org.biojava3.core.sequence.transcription

RNASequence
RNASequence where RNACompoundSet are the allowed values