Uses of Package
org.biojava.nbio.core.sequence

Packages that use org.biojava.nbio.core.sequence

Package	Description
org.biojava.nbio.aaproperties	Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat	Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor	Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.core.alignment
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.util
org.biojava.nbio.genome
org.biojava.nbio.genome.homology
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.
org.biojava.nbio.genome.parsers.geneid
org.biojava.nbio.genome.parsers.gff
org.biojava.nbio.genome.util
org.biojava.nbio.phylo
org.biojava.nbio.ronn	BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.ws.hmmer

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.aaproperties

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.aaproperties.profeat

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.aaproperties.profeat.convertor

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.core.alignment

Class and Description
AccessionID Used in Sequences as the unique indentifier.

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.io

Class and Description
DNASequence This is class should model the attributes associated with a DNA sequence
GeneSequence
ProteinSequence The representation of a ProteinSequence
RNASequence RNASequence where RNACompoundSet are the allowed values

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.loader

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.location

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.location.template

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.storage

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.template

Class and Description
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.biojava.nbio.core.sequence used by org.biojava.nbio.core.sequence.transcription

Class and Description
RNASequence RNASequence where RNACompoundSet are the allowed values

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.core.util

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome

Class and Description
ChromosomeSequence A ChromosomeSequence is a DNASequence but keeps track of geneSequences
DNASequence This is class should model the attributes associated with a DNA sequence
GeneSequence
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome.homology

Class and Description
GeneSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome.io.fastq

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

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome.parsers.geneid

Class and Description
DNASequence This is class should model the attributes associated with a DNA sequence
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome.parsers.gff

Class and Description
ChromosomeSequence A ChromosomeSequence is a DNASequence but keeps track of geneSequences
DNASequence This is class should model the attributes associated with a DNA sequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.genome.util

Class and Description
DNASequence This is class should model the attributes associated with a DNA sequence
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.phylo

Class and Description
MultipleSequenceAlignment Implements a minimal data structure for reading and writing a sequence alignment.

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.ronn

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.structure.align.multiple.util

Class and Description
MultipleSequenceAlignment Implements a minimal data structure for reading and writing a sequence alignment.
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.structure.cluster

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.structure.io

Class and Description
ProteinSequence The representation of a ProteinSequence

Classes in org.biojava.nbio.core.sequence used by org.biojava.nbio.ws.hmmer

Class and Description
ProteinSequence The representation of a ProteinSequence