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I10: Homologous Recombination



  1. A DNA fragment with homology arms on the both ends, replaces the genomic regions which are wedged between same homologous arm sequences.
    • The features on the sequence of the recombinant fragment are also inherited to the transformed genomic sequence.




  • Homology score settings of homology arm



Input File Format


  • Target genomic sequence file
    • This file should be loaded on the current sequence folder, and specified as the current sequence.



  • Recombinant fragment sequence file
    • This file should be loaded on the current reference folder.


Result Format


  • Recombinant genomic sequence file
    • A recombinant genomic sequence file is generated as a new file. This file can be load on the current folder by one click.




  1. Previous to the homologous recombination operation, a recombinant fragment file should be attached with homology arms on the both ends of the sequence.




  1. Load the genomic sequence file and make it as the current sequence.
  2. From the menu, click "Cloning" --> "Homologous Recombination".
    • Homologous recombination dialog is displayed.
  3. Click "Insert Fragment" field.
    • The candidate list of insert fragments is displayed.
    • The list includes all the sequence files which are loaded on the Reference Folder.
    • Multiple selection of fragments are allowed to be selected and simultaneously transformed in more than one recombinant regions of the genome.
    • Check on "Reverse Complement", the reverse complement sequence of the fragment sequence are recombined.
  4. Click "Run".
    • The homologous recombination is performed.
    • The genomic sequence replaced with the recombinant fragment sequence is generated in GenBank format.
    • The file is named as "recombination999999999.gbk".
  5. Click "Load".
    • The recombinant genomic sequence file is loaded on the current sequence folder and displayed as the current sequence on the feature map.


Future Enhancement and Improvement


  1. Automatic attachment of homology arm
    • A recombined region is specified by dragging the target region of the genomic sequence, then homology arms are designed on the both end of region and the arms are attached to the both ends of the recombinant fragment sequence.


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