예제 #1
0
  /** Generation of new BioBricks primers for parts * */
  public static String[] generateVectorPrimers(
      RVector vector,
      Collector coll,
      Double meltingTemp,
      Integer targetLength,
      Integer maxPrimerLength,
      Integer minPCRLength) {

    // initialize primer parameters
    String[] oligos = new String[2];
    String vectorPrimerPrefix = "gaattcgcggccgcttctagag";
    String vectorPrimerSuffix = "tactagtagcggccgctgcag";

    Vector currentVector = coll.getVector(vector.getUUID(), true);
    String seq = currentVector.getSeq();
    String fwdHomology;
    String revHomology;
    if (seq.equals("")) {
      fwdHomology = "[ VECTOR " + currentVector.getName() + " HOMOLOGY REGION ]";
      revHomology = "[ VECTOR " + currentVector.getName() + " HOMOLOGY REGION ]";
    } else {
      fwdHomology =
          seq.substring(
              0,
              Math.min(
                  seq.length(),
                  PrimerDesign.getPrimerHomologyLength(
                      meltingTemp, targetLength, maxPrimerLength - 23, minPCRLength, seq, true)));
      revHomology =
          PrimerDesign.reverseComplement(
              currentVector
                  .getSeq()
                  .substring(
                      Math.max(
                          0,
                          seq.length()
                              - PrimerDesign.getPrimerHomologyLength(
                                  meltingTemp,
                                  targetLength,
                                  maxPrimerLength - 22,
                                  minPCRLength,
                                  PrimerDesign.reverseComplement(seq),
                                  true))));
    }

    String forwardOligoSequence = vectorPrimerPrefix + fwdHomology;
    String reverseOligoSequence = PrimerDesign.reverseComplement(vectorPrimerSuffix) + revHomology;

    oligos[0] = forwardOligoSequence;
    oligos[1] = reverseOligoSequence;

    return oligos;
  }
예제 #2
0
  /** Generation of new BioBricks primers for parts * */
  public static String[] generatePartPrimers(
      RNode node,
      Collector coll,
      Double meltingTemp,
      Integer targetLength,
      Integer minPCRLength,
      Integer maxPrimerLength) {

    // initialize primer parameters
    String[] oligos = new String[2];
    String partPrimerPrefix = "gaattcgcggccgcttctagag";
    String partPrimerSuffix = "tactagtagcggccgctgcag";
    String partPrimerPrefixAlt = "gaattcgcggccgcttctag";
    String forwardOligoSequence;
    String reverseOligoSequence;

    Part currentPart = coll.getPart(node.getUUID(), true);
    String seq = currentPart.getSeq();
    ArrayList<String> type = node.getType();
    String fwdHomology;
    String revHomology;

    // If the part is sufficiently large
    if (seq.length() > minPCRLength) {

      // Special case primers for coding sequences
      if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {
        fwdHomology =
            seq.substring(
                0,
                Math.min(
                    seq.length(),
                    PrimerDesign.getPrimerHomologyLength(
                        meltingTemp, targetLength, maxPrimerLength - 20, minPCRLength, seq, true)));
        revHomology =
            seq.substring(
                Math.max(
                    0,
                    currentPart.getSeq().length()
                        - PrimerDesign.getPrimerHomologyLength(
                            meltingTemp,
                            targetLength,
                            maxPrimerLength - 21,
                            minPCRLength,
                            PrimerDesign.reverseComplement(seq),
                            true)));
        forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
        reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);

      } else {
        if (seq.equals("")) {
          fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
          revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
        } else {
          fwdHomology =
              seq.substring(
                  0,
                  Math.min(
                      seq.length(),
                      PrimerDesign.getPrimerHomologyLength(
                          meltingTemp,
                          targetLength,
                          maxPrimerLength - 22,
                          minPCRLength,
                          seq,
                          true)));
          revHomology =
              seq.substring(
                  Math.max(
                      0,
                      currentPart.getSeq().length()
                          - PrimerDesign.getPrimerHomologyLength(
                              meltingTemp,
                              targetLength,
                              maxPrimerLength - 21,
                              minPCRLength,
                              PrimerDesign.reverseComplement(seq),
                              true)));
        }
        forwardOligoSequence = partPrimerPrefix + fwdHomology;
        reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);
      }

      // Otherwise make annealing primers or synthesize
    } else {
      if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {

        if (seq.equals("")) {
          fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
          revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
          forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
          reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
        } else {
          fwdHomology = seq;
          forwardOligoSequence = partPrimerPrefixAlt + fwdHomology + partPrimerSuffix;
          reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
        }

      } else {

        if (seq.equals("")) {
          fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
          revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
          forwardOligoSequence = partPrimerPrefix + fwdHomology;
          reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
        } else {
          fwdHomology = seq;
          forwardOligoSequence = partPrimerPrefix + fwdHomology + partPrimerSuffix;
          reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
        }
      }
    }

    oligos[0] = forwardOligoSequence;
    oligos[1] = reverseOligoSequence;

    return oligos;
  }