Uses of Class
bacnet.datamodel.sequence.Gene
Packages that use Gene
Package
Description
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Uses of Gene in bacnet.datamodel.sequence
Subclasses of Gene in bacnet.datamodel.sequenceMethods in bacnet.datamodel.sequence that return GeneModifier and TypeMethodDescriptionChromosome.getGeneDownstream(Gene gene) Return the gene downstreamGene.getGeneDownstream()Return the gene downstream on the + strandGenome.getGeneFromName(String name) Go through all chromosomes and each Genes map and GeneName map to find the corresponding geneGenome.getGeneFromName(String name, String accessionChromo) Go through all chromosomes and each Genes map and GeneName map to find the corresponding geneGenome.getGeneFromProteinId(String proteinId) Go through all chromosomes and Gene from corresponding proteinidChromosome.getGeneUpstream(Gene gene) Return the gene upstreamGene.getGeneUpstream()Return the gene upstream on the + strandstatic GeneLoad a serialized GeneMethods in bacnet.datamodel.sequence that return types with arguments of type GeneModifier and TypeMethodDescriptionChromosome.getGenes()Genome.getGenes()Return all Genes in all chromosomesChromosome.getGenesAlternative()Methods in bacnet.datamodel.sequence with parameters of type GeneModifier and TypeMethodDescriptionChromosome.getGeneDownstream(Gene gene) Return the gene downstreamChromosome.getGeneUpstream(Gene gene) Return the gene upstreamMethod parameters in bacnet.datamodel.sequence with type arguments of type GeneModifier and TypeMethodDescriptionvoidChromosome.setGenes(LinkedHashMap<String, Gene> genes) voidChromosome.setGenesAlternative(LinkedHashMap<String, Gene> genesAlternative) -
Uses of Gene in bacnet.datamodel.sequenceNCBI
Methods in bacnet.datamodel.sequenceNCBI that return GeneModifier and TypeMethodDescriptionstatic GeneGenomeConversionElement.convertDNASequenceGene(DNASequence dnaSeq) From a DNASequence make a Gene object -
Uses of Gene in bacnet.reader
Method parameters in bacnet.reader with type arguments of type GeneModifier and TypeMethodDescriptionstatic voidSave all amino acid sequence in a fasta filestatic voidFastaFileReader.saveProteins(ArrayList<Gene> sequences, String fileName) Save all amino acid sequence in a fasta filestatic voidPTTReader.saveProteins(ArrayList<Gene> sequences, String fileName, Chromosome chromo) Save list of Gene in a PTT file
Information about the resulting protein are written into different columns:
"Location","Strand","Length","PID","Gene","Synonym","Code","COG","Product" -
Uses of Gene in bacnet.scripts.genome
Methods in bacnet.scripts.genome with parameters of type GeneModifier and TypeMethodDescriptionstatic StringSDProfile.verifyGene(Gene gene, String[][] arrayPlus, String[][] arrayMinus) For a given Gene calculate its SD binding energy, and compare to the value given by SDProfile data -
Uses of Gene in bacnet.scripts.listeriomics.nterm
Methods in bacnet.scripts.listeriomics.nterm that return types with arguments of type GeneMethods in bacnet.scripts.listeriomics.nterm with parameters of type GeneModifier and TypeMethodDescriptionString[]NTermStat.getAtisBHI(Gene gene) Go through all MassSpec data and find if the lmio was detectedNTermStat.getAtisBlood(Gene gene) After generating TIRSequence.fasta in setTIRSequence() method we submit to http://genomes.urv.cat/CAIcal/ to calculate CAI value and expected CAI value The table with CAI values is saved from the website in: CAIResults.excelNTermStat.getCAIGene(Gene gene) After generating GeneSequence.fasta in setGeneSequence() method we submit to http://genomes.urv.cat/CAIcal/ to calculate CAI value and expected CAI value The table with CAI values is saved from the website in: StatGenes/CAIGeneResults.excelintNTermStat.getChargedResidues(Gene gene, int decay) Sum up the different charge of the amino acids of the TIRintNTermStat.getChargedResiduesGene(Gene gene) Sum up the different charge of the amino acids of the gene sequencestatic StringNTermStat.getComment(Gene gene) Return information about gene or iTISNTermStat.getDetectable(Gene gene) By reading the List in: /StatGenes/EGDeDetectable.txt Say if a gene is detectable by the spectometer or notdoubleNTermStat.getGeneExpr(Gene gene, String dataName) Return the median value expression (calculated on 10 BHI 37C data) in the Gene Expression array of the geneNTermStat.getNCRNAUpstream(Gene gene) For each gene search if the end of a smallRNA or cisReg element is in the region -200bp - start codonstatic StringNTermStat.getSDEnergy(Gene gene) Return the binding energy with aSD sequencestatic doubleNTermStat.getStartCodon(Gene gene) Return start codon proportion in the genomestatic StringNTermStat.getTIRStructureEnergy(Gene gene) For very gene read TIRStructure.excel and extract the mean value of energy: We calculate the 2nd structure free energy and save it a table
And we calculate the energy for 40 different sequence: -20+40 to -20+80 and calculate the average energyintNTermStat.getTotalSpectrum(Gene gene) For each gene add the number of spectra of every peptide available (not only aTIS peptides)intNTermStat.getUTRLength(Gene gene) Deprecated. -
Uses of Gene in bacnet.scripts.listeriomics.srna
Method parameters in bacnet.scripts.listeriomics.srna with type arguments of type GeneModifier and TypeMethodDescriptionstatic voidSmallPeptidesSearch.multiSpeciesAlignBlastN(ArrayList<Gene> genes) Deprecated. -
Uses of Gene in bacnet.sequenceTools
Methods in bacnet.sequenceTools that return GeneMethods in bacnet.sequenceTools with parameters of type GeneModifier and TypeMethodDescriptionstatic voidGeneView.displayGene(Gene gene, org.eclipse.e4.ui.workbench.modeling.EPartService partService) Display a given genestatic StringGeneViewHomologTools.getPhyloFigure(Gene sequence, ArrayList<String> genomeNames) Read Phylogenomic figure and modify the labels with homolog tablestatic voidGeneViewHomologTools.loadFigureHomologs(Gene sequence, org.eclipse.swt.browser.Browser browserHomolog, ArrayList<String> selectedGenomes) Load SVG figure of phylogeny and replace all strain name by homolog informations
Save to JPG file and display itvoidGeneView.setSequence(Gene sequence)