Package org.biojava.nbio.core.sequence
package org.biojava.nbio.core.sequence
-
ClassDescriptionUsed in Sequences as the unique indentifier.BasicSequence<C extends Compound>Bare bones version of the Sequence object to be used sparingly.Represents a exon or coding sequence in a gene.A ChromosomeSequence is a DNASequence but keeps track of geneSequencesGenBank 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|identifierThis is class should model the attributes associated with a DNA sequenceThe type of DNA sequenceSort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.A gene contains a collection of Exon sequencesImplements a minimal data structure for reading and writing a sequence alignment.The representation of a ProteinSequenceRNASequence where RNACompoundSet are the allowed valuesUsed to sort sequencesA static class that provides optimization hints for memory or performance handling of sequence data.Used to map the start codon feature on a geneUsed to map the stop codon sequence on a geneProvides a way of representing the strand of a sequence, location hit or feature.A sequence can be associated with a species or Taxonomy IDThis is the sequence if you want to go from a gene sequence to a protein sequence.