Adding a Local Sequence File

To add a local sequence file to SeqWeb, the file must first reside on the computer from which you are running the web browser. You may need to transfer the sequence files, for example via FTP, to your PC or Macintosh. For information about transferring files, see your system manager.

You can load sequences into SeqWeb from within the Sequence Manager or from within a program.

1. Choose from the following.
   • From the Sequence Manager:
     1. Under Sequence Manager Functions, click Add.

     2. On the right of the sequence list, click Local File.

   • From within a program, locate the Input Sequence area and click Local File.

     The Add Local File window appears.

2. Choose from the following:
   • If you know the name and location of the sequence of interest, type its directory and filename specification in the text box.

   • If you are unsure of the sequence name and location:
     1. Click Browse...

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        The File Upload dialog box (Netscape) or Choose file dialog box (Internet Explorer) appears.

     2. Navigate the directories and select the sequence "c:/Bio/naq.txt or psq.txt".
     3. Click Open.

        The dialog box disappears and the selected sequence filename and its directory specification display in the text box.

• In the Add Local File window, click OK.

  Copying and Pasting Sequences from the Clipboard

  You can copy and paste sequences into SeqWeb from within the Sequence Manager or from within a program.

  1. Choose from the following.
     • From the Sequence Manager:
       1. Under Sequence Manager Functions, click Add.

       2. On the right of the sequence list, click Clipboard.

     • From within a program, locate the Input Sequence area and click Clipboard.

       The Add from Clipboard window appears.

  2. Type or copy and paste information into the following fields:

     Name: TVCDC-NAQ

     Description Line: (optional) A brief description of the sequence. This description will appear in the status bar at the bottom of the browser window when you select a sequence in SeqWeb.

     Reference: (optional) Additional sequence comments and reference information.

     Sequence Data: (required) The sequence residues. May contain alphanumeric characters or spaces.

     To copy and paste on a PC :

     1. Open the file c:/Bio/naq.txt or psq.txt In a separate window, display the sequence of interest.

     2. Click and drag over the text of interest to highlight it.

     3. From the window's Edit menu, select Copy.

     4. Bring your SeqWeb window to the front and click in the text area where you want to paste the text.

     5. Click and hold your right mouse button to display a menu of commands.

     6. Select Paste.

        The text is pasted into the area.

     To copy and paste on UNIX:

     1. In a separate window, display the sequence of interest.

     2. Click and drag over the text of interest to highlight it.

     3. Bring your SeqWeb window to the front.

     4. Click your right mouse button in the appropriate text area.

        The text is pasted into the area.

  3. In the Add from Clipboard window, click OK.

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  Loading Database Sequences

  You can load database sequences into SeqWeb from within the Sequence Manager or from within a program.

  1. Choose from the following:
     • From the Sequence Manager:
       1. Under Sequence Manager Functions, click Add.

       2. On the right of the sequence list, click Database.

     • From within a program, locate the Input Sequence area and click Database.

       The Add from Database window appears.

  2. Select the appropriate database from the Database selection menu.

     The databases available are determined by your site's GCG system manager.

  3. In the Sequence name or accession number text box, type the sequence name (for example eg15_caeel) or its accession number (for example Q10656). Or use the * wildcard to find multiple sequences, for example eg15_ca*.
     TYPE L10131 in the Accession Number Field

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  4. Click OK.

     SeqWeb displays sequence(s) with matching name(s).

  5. Select the sequence(s) of interest. Choose from the following:
     • To select all sequences, click Select All in the bottom frame.

       If the results contain multiple pages, you must load each separate page and click Select All.

     • To select individual sequences, click the checkbox to the left of each sequence of interest.

     • To clear all selected sequences, click Deselect All.

  6. Click Add Selected.

     The sequences are loaded into the Sequence Manager list.

Creating a New Sequence

You can create a new sequence from within the Sequence Manager or from within a program.

1. Choose from the following.
   • From the Sequence Manager:
     1. Under Sequence Manager Functions, click Add.

     2. On the right of the sequence list, click Clipboard.

   • From within a program, locate the Input Sequence area and click Clipboard.

     The Add from Clipboard window appears.

2. Type or copy and paste information into the following text boxes:

   Name: (required) The sequence name.

   Description Line: (optional) A brief description of the sequence. This description will appear in the status bar at the bottom of the browser window when you select a sequence in SeqWeb.

   Reference: (optional) Additional sequence comments and reference information.

   Sequence Data: (required) The sequence residues. May contain alphanumeric characters or spaces.

3. In the Add from Clipboard window, click OK.

   The sequence is loaded into the Sequence Manager list.

Editing and Documenting Sequences

SeqWeb lets you edit sequences in the following ways:

• rename a sequence (use the Rename function).

• add, delete, or change sequence residues (use Edit).

• specify a new sequence length by deleting residues at a sequence's beginning or ending (use Edit).

  If you want to keep the original sequence intact, use Copy to create a duplicate sequence, then modify the copy's residues.

• change the sequence type from nucleotide to protein if SeqWeb guesses incorrectly at its makeup (use Edit).

• add a sequence description for documentation purposes (use Edit).

Note SeqWeb does not provide a way to edit multiple sequence alignments. To do so, use SeqLab or the command-line interface to the Wisconsin Package.

Renaming a Sequence

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1. Select Sequence Manager.

   The Sequence Manager page loads.

2. Under Sequence Manager Functions, click Rename.

   SeqWeb displays a list of your currently loaded sequences.

3. Select a sequence from the list.

   The sequence's description displays in the status line at the bottom of the browser window.

4. Click the Rename button on the right of the sequence list.

   The Rename window appears.

5. Type the new name of the sequence in the Name text box.

6. Click OK.

   The renamed sequence appears in the sequence list.

Editing Sequences

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1. Select Sequence Manager.

   The Sequence Manager page loads.

2. Under Sequence Manager Functions, click Edit.

   SeqWeb displays a list of your currently loaded sequences.

3. Select a sequence from the list.

   The sequence's brief description displays in the status line at the bottom of the browser window.

4. Click the Edit button on the right of the sequence list.

   The Edit window appears, displaying the sequence's full description, reference, and sequence data.

5. Edit the information in the following fields:

   Type: (required) Defines the sequence as nucleic (N) or protein (P).

   Description Line: (optional) A brief description of the sequence. This description will appear in the status bar at the bottom of the browser window when you select a sequence in SeqWeb.

   Reference: (optional) Additional sequence comments and reference information.

   Sequence Data: (required) The sequence residues. When editing sequence data, you can ignore the numbers to the left of each line of data. SeqWeb automatically renumbers and reformats the sequence when you click OK.

6. Click OK.

Copying Sequences

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You may want to use the Copy function to create multiple versions of the same sequence, each with a different sequence length (begin and end residue ranges) or with changed residues.

1. Select Sequence Manager.

   The Sequence Manager page loads.

2. Under Sequence Manager Functions, click Copy.

   SeqWeb displays a list of your currently loaded sequences.

3. Select a sequence from the list.

   The sequence description displays in the status line at the bottom of the browser window.

4. Click the Copy button on the right of the sequence list.

   The Copy window appears.

5. Type a new name for the sequence copy in the Name text box.

6. Click OK.

   The newly copied sequence appears in the sequence list.

   See "Editing and Documenting Sequences" in Chapter 3, The Sequence Manager

Viewing Sequences

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By clicking on a sequence name, you can view its brief description in the status line at the bottom of the browse. To view the full sequence description, reference, and residues, use the View function in the Sequence Manager.

1. Select Sequence Manager.

   The Sequence Manager page loads.

2. Under Sequence Manager Functions, click View.

   SeqWeb displays a list of your currently loaded sequences.

3. Select a sequence from the list.

   The sequence description displays in the status line at the bottom of the browser window.

4. Click the View button on the right of the sequence list.

   The View window appears, displaying the contents of the sequence.

5. Click Close to close the View window.

Deleting Sequences

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1. Select Sequence Manager.

   The Sequence Manager page loads.

2. Under Sequence Manager Functions, click Delete.

   SeqWeb displays a list of your currently loaded sequences.

3. Select one or more sequences.

   The sequence description displays in the status line at the bottom of the browser window.

4. Click the Delete button on the right of the sequence list.

   SeqWeb asks you to confirm the deletion, then deletes the selected sequences from the server.