Package org.biojava.nbio.core.sequence

Class TranscriptSequence

java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava.nbio.core.sequence.DNASequence
org.biojava.nbio.core.sequence.TranscriptSequence
All Implemented Interfaces:
Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>
public class TranscriptSequence extends DNASequence
This is the sequence if you want to go from a gene sequence to a protein sequence. Need to start with a ChromosomeSequence then getting a GeneSequence and then a TranscriptSequence
Author:
Scooter Willis

  • Constructor Details

    • TranscriptSequence

      public TranscriptSequence(GeneSequence parentDNASequence, int begin, int end)
      Parameters:
      parentDNASequence -
      begin -
      end - inclusive of end

  • Method Details

    • getLength

      public int getLength()
      Description copied from interface: Sequence
      Returns the length of the Sequence
      Specified by:
      getLength in interface Sequence<NucleotideCompound>
      Overrides:
      getLength in class AbstractSequence<NucleotideCompound>

    • getStrand

      public Strand getStrand()
      Returns:
      the strand

    • removeCDS

      public CDSSequence removeCDS(String accession)
      Remove a CDS or coding sequence from the transcript sequence
      Parameters:
      accession -
      Returns:

    • getCDSSequences

      public LinkedHashMap<String,CDSSequence> getCDSSequences()
      Get the CDS sequences that have been added to the TranscriptSequences
      Returns:

    • addCDS

      public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws Exception
      Add a Coding Sequence region with phase to the transcript sequence
      Parameters:
      accession -
      begin -
      end -
      phase - 0,1,2
      Returns:
      Throws:
      Exception

    • getProteinCDSSequences

      public ArrayList<ProteinSequence> getProteinCDSSequences()
      Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet. This can be used to map a CDS/exon region of a protein sequence back to the DNA sequence If you have a protein sequence and a predicted gene you can take the predict CDS protein sequences and align back to the protein sequence. If you have errors in mapping the predicted protein CDS regions to an the known protein sequence then you can identify possible errors in the prediction
      Returns:

    • getDNACodingSequence

      public DNASequence getDNACodingSequence()
      Get the stitched together CDS sequences then maps to the cDNA
      Returns:

    • getProteinSequence

      public ProteinSequence getProteinSequence()
      Get the protein sequence
      Returns:

    • getProteinSequence

      public ProteinSequence getProteinSequence(TranscriptionEngine engine)
      Get the protein sequence with user defined TranscriptEngine
      Parameters:
      engine -
      Returns:

    • getStartCodonSequence

      public StartCodonSequence getStartCodonSequence()
      Returns:
      the startCodonSequence

    • addStartCodonSequence

      public void addStartCodonSequence(AccessionID accession, int begin, int end)
      Parameters:
      startCodonSequence - the startCodonSequence to set

    • getStopCodonSequence

      public StopCodonSequence getStopCodonSequence()
      Returns:
      the stopCodonSequence

    • addStopCodonSequence

      public void addStopCodonSequence(AccessionID accession, int begin, int end)
      Parameters:
      stopCodonSequence - the stopCodonSequence to set