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GenBank Searching and Importing |
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Gene Construction Kit has comprehensive features to allow GenBank searching and file retrieval over the Internet with importing directly into GCK. All GenBank features are converted one-to-one to GCK features using a conversion scheme you can customize. The following tutorial illustrates some of the new features. Images alternate between Mac and Windows screenshots. The program works the same way on each platform.
1. Open Gene Construction Kit. Choose File > Deluxe > Import > Conversion Defaults. This will bring up the Figure 1.
Figure 1
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The conversion defaults shown in this window define how the different features listed in the GenBank features table will be converted to Gene Construction Kit features. If you do not see this window, then choose File > Deluxe Import > Restore Defaults and select the file called Importing Defaults; then save the Conversion defaults using File > Deluxe Import > Save Defaults.
Each item in the list on the left has four columns of information. The Use column defines whether or not that particular type of feature should be used in converting GenBank files into GCK files. It can contain a check mark for 'yes' or an 'x' for 'no'. Clicking on the check mark or the x will toggle the item between the two possibilities. If you don't use a feature, its information will still be stored in the General Info for the construct and can be viewed at a later time. The Name column is the name of the feature as defined by NCBI for GenBank features. As you click on each feature name, you will see the NCBI definition in the right Description "pane" of this window. The Type column indicates the kind of GCK feature that will be used to display the GenBank feature entry. These types are the standard ways of displaying sequence "adornments" within GCK (see Figure 2). The final column, Format, indicates how the feature will actually be displayed within GCK.
You can click on any item in the list on the left and a description will appear on the right in the "Description" box. Once you have selected an item in the list, you can change the appearance of the GCK feature by using any of the available choices in the Format menu in GCK. Try changing the appearance of some of the features in the list using the options in the Format menu.
Figure 2
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If you do not like a default assignment (mapping) of a GenBank feature to a GCK feature, you can assign a different GCK feature by choosing an item from the Feature menu (Figure 2). Select an item in the list and then choose how you would like to represent that item in GCK from the Feature menu. Once you have selected the GCK feature, it will be displayed in the Conversion Defaults dialog box (Figure 1) where you can specify its properties. If you would like to save the Conversion Defaults, choose File > Deluxe Import > Save Conversion Defaults. This will allow you to save the conversions as a file that you can access later on. It is possible to save multiple "conversion files", each containing different sets of conversions. Using File > Deluxe Import > Restore Conversion Defaults will allow you to choose one for use as the default conversion table on you computer. Close the Conversion Defaults window.
2. Choose File > Deluxe Import > Open Sequence File and open the file named gbmam_sample.gbk. This file was downloaded from GenBank and contains several different sequences in the same document. When you open the file, you will see Figure 3. The five different sequence entries in this file are listed in the Entries column. When one of the entries is selected (e.g. BTBAINH1), the features from the features table are listed in the Features column. Finally, when one of he features is selected (e.g. enhancer), the information relevant to that feature is displayed in the Source box. The transfer preferences lets you define how you want the program to behave for this conversion operation. Open it now to see what choices you have.
Figure 3
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3. Press the "Convert to GCK" button. This will bring up Figure 4. This window shows the features that are available for the particular DNA being imported. In this case, the 5' UTR and exon features have been turned off and will not be shown in the resulting GCK construct. The conversions visible here are the result of using the Conversion Defaults, but you can still change them to whatever you wish.
Figure 4
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4. Press the "Save Construct" button. Depending on how you set your transfer preferences, you may automatically (or through a dialog box or two) see Figure 5, which is the new GCK construct window. This shows how the new features have been mapped out for this particular sequence.
Figure 5
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These steps have demonstrated how you can import a GenBank file that you already have available into GCK.
The following steps will demonstrate how to search and retrieve sequences from GenBank and have them automatically imported into GCK.
5. To perform the following, you need to be connected to the Internet. If you are not already on line, please connect now. Choose File > Deluxe Import > Retrieve Sequence and enter ''J00231" (or any other accession number or sequence name you might be interested in) into the box in the top left corner, as shown in Figure 6.
Figure 6
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As you enter the accession number or sequence name into this box, you can see a URL being constructed in the bottom left box (this is not editable, but is shown for you to examine). This URL will be sent to the server that you have designated. GenBank and EMBL are default buttons, but you can also specify a specific internal server by pressing the Set Root URL... button. Pressing Retrieve will contact your target database and retrieve the sequence for you. Once the sequence is retrieved, you will see a window very much like that shown in Figure 3. You can proceed from that point to finish importing the sequence into GCK using the same steps described above.
6. You can also search GenBank using GCK. Selecting File > Deluxe Import > Search GenBank will bring up Figure 7, which shows the search dialog for defining how you want to search GenBank.
Figure 7
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Note that the popup menu allows you to define the database fields to be searched by your query. Type in the search expression you wish to look for and then press the Search button. A progress dialog informs you of progress, and then you will get a list of items matching your query. The list will be similar to Figure 3. The sequences you are interested in are now on your hard disk and can be imported directly into GCK.
8. If your DNA source file has entries in the features table that might be ambiguous, you will see a button that says Location Prefs.... Pressing this button will bring up Figure 8, allowing you to define how you want the feature locations to be interpreted. This window lists the possible ways in which various features are defined by NCBI for use in GenBank files. Some of these are not directly translatable into GCK features, so you can define how you want to handle those situations in this window.
Figure 8
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9. Feel free to try different operations using the deluxe importer. The searching works the same way as an Entrez search would work at the NCBI web site.
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