Tutorial: Importing and Exporting Sequences and Other Information

One often obtains sequences in other formats and would like to work with them in GCK. This can be done by importing the sequences into GCK. Most other formats really are just plain text files with the sequence information organized in a specific format. Perhaps the most common of these formats is GenBank or GCG format. Just a plain sequence file (nothing but sequence) is also fairly common and is often the form of the output you might get from a sequencing facility.

  1. Start GCK and choose File > Import to begin the importing process. You will see something like Figure 2.63. Use the popup menu above the list of files to navigate to the DNAs to import folder which was installed when GCK was installed. This folder holds DNAs in a number of different file formats for you to test importing. The radio buttons in this dialog allow you to specify in which file format you believe the file to be. Clicking on the radio button might also change the list of files that are visible. Gene Inspector and DNA Inspector files are not plain text files so clicking on one of those buttons will limit the list of displayed files to just those specific types of (non-text) files.
    Figure 2.63: Import Sequence Dialog
  2. Click on the GCG button and select the file DNA.GCG to be imported as shown in Figure 2.63. Press Import.
  3. The sequence will now be imported and displayed as a sequence in a new Construct window. Any comments associated with the text file in the specified format will be imported and placed in the General Info for the construct. Choose Construct > General Info… to see the comments that were part of this particular GCG formatted file.
  4. Gene Inspector® files might contain multiple sequences, so you will be presented with a dialog like Figure 2.64. This shows the dialog presented when a file containing multiple sequences is selected. You must choose one of the sequences and then press Import.
    Figure 2.64: Importing Sequences from Gene Inspector
  5. Exporting file information is another way GCK can interact with other applications. Since GCK can display information in graphical as well as sequence formats, both formats are available to export. Choose File > Open… and open pBR322 in the tutorial files folder. This will open a graphical view.
  6. [NOTE – if working with the demo version of GCK, exporting is disabled – so you will not be able to carry out the remaining steps of this Tutorial, but feel free to read through the details about exporting options. If you plan on continuing on to the next Tutorial, please close this file without saving the changes.]
  7. If working with a ‘Trial Version’ or the ‘Full Version’ of the application, choose File > Export… and you will see Figure 2.65. Choosing the JPEG file popup menu as shown here will create a file that can be imported into most graphics programs. The DNA Sequence as TEXT file button will create a text only file of the DNA sequence which can be opened by any word processing program as well as almost any other sequence analysis package. Click Cancel to dismiss this dialog unless you are really interested in playing with the output files in other programs.
    Figure 2.65: Export (Graphics)
  8. With the pBR322 window active, choose Construct > Display > Display Sequence to change the construct view to a sequence listing. Now, choosing File > Export… will bring up a slightly different dialog, Figure 2.66. In this case, there is an extra option called Formatted Listing as TEXT file. This option will produce a text file containing all the line numbers, restriction sites, spacing, and amino acid sequences. Note that in order to view these output files correctly formatted in another application, you will need to use a monospaced font like Monaco or Courier.
    Figure 2.66: Export (Sequence)

This concludes this tutorial. You can close the open window (don’t save changes – you will not need this file any more).

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