/** Converts the DNA sequence to protein sequence. * * @param dnaSequence the DNA sequence * * @return the protein sequence */ public static ProteinSequence convertDNAtoProteinSequence(DNASequence dnaSequence) throws CompoundNotFoundException { RNASequence mRNA = dnaSequence.getRNASequence(); return mRNA.getProteinSequence(); } }
/** * Get the ProteinSequence from the RNA sequence * @return */ public ProteinSequence getProteinSequence() { return getProteinSequence(TranscriptionEngine.getDefault()); }
/** * Get the ProteinSequence from the RNA sequence * @return */ public ProteinSequence getProteinSequence() { return getProteinSequence(TranscriptionEngine.getDefault()); }
public static void main(String[] args) throws Exception { LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(new File("src/test/resources/NM_000266.gb"), true); for (DNASequence sequence : dnaSequences.values()) { logger.info("DNA Sequence: {}", sequence.getRNASequence().getProteinSequence().getSequenceAsString()); } LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankReaderHelper.readGenbankProteinSequence(new File("src/test/resources/BondFeature.gb"), true); for (ProteinSequence sequence : proteinSequences.values()) { logger.info("Protein Sequence: {}", sequence.getSequenceAsString()); } } }
public static void main(String[] args) throws Exception { LinkedHashMap<String, DNASequence> dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("fasta.fna")); for (DNASequence sequence : dnaSequences.values()) { sequence.getRNASequence().getProteinSequence().getSequenceAsString(); } } }
public static void main(String[] args) throws Exception { LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(new File("src/test/resources/NM_000266.gb"), true); for (DNASequence sequence : dnaSequences.values()) { logger.info("DNA Sequence: {}", sequence.getRNASequence().getProteinSequence().getSequenceAsString()); } LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankReaderHelper.readGenbankProteinSequence(new File("src/test/resources/BondFeature.gb"), true); for (ProteinSequence sequence : proteinSequences.values()) { logger.info("Protein Sequence: {}", sequence.getSequenceAsString()); } } }
public static void main(String[] args) throws Exception { LinkedHashMap<String, DNASequence> dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("fasta.fna")); for (DNASequence sequence : dnaSequences.values()) { sequence.getRNASequence().getProteinSequence().getSequenceAsString(); } } }
ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(TranscriptionEngine.getDefault()); proteinSequence.setAccession(new AccessionID(cdsSequence.getAccession().getID())); proteinSequence.setParentDNASequence(cdsSequence, 1, cdsSequence.getLength());
ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(TranscriptionEngine.getDefault()); proteinSequence.setAccession(new AccessionID(cdsSequence.getAccession().getID())); proteinSequence.setParentDNASequence(cdsSequence, 1, cdsSequence.getLength());
/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }
/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }