Chapter 2. SeqWeb Basics

About SeqWeb Managers

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SeqWeb provides a set of Managers to assist you with performing your tasks and managing your work. Each of these Managers is described in more detail in subsequent chapters. Briefly, the SeqWeb Managers are as follows:

	The Sequence Manager is for adding, creating, editing, copying, viewing, and saving sequences. It also provides access to project management functions.
	The Job Manager is primarily for monitoring jobs (program runs).
	The Results Manager is for viewing and managing program results.
	The Preferences Manager is for managing your SeqWeb settings.

Some sites may also have a Subsets Manager, which is for building, editing, and deleting SeqStore subsets. This manager is only described in the online help that accompanies that option.

To access the SeqWeb Managers:

1. Click the Managers button in the top left SeqWeb frame.

   The icons for the SeqWeb Managers display in the lower left frame.

2. Click the icon in the lower left frame for the Manager you want to use.

About Projects

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It is important to understand that SeqWeb associates sequence data and analysis results with a specific project. Each project has a textual description, sequence data, analysis results, and team members associated with it. Your SeqWeb Administrator will provide you with a "Default" project to get you started. You may also have the ability to create additional projects. If so, SeqWeb allows you to organize and maintain your sequence data and analysis results according to those projects. For more information about whether or not your account allows for multiple projects, contact your SeqWeb Administrator.

The currently selected project will determine which sequences and/or results are available to you. When running a program, only the sequences associated with the currently selected project appear in the program's Input Sequence list. When using the Results Manager, only the results associated with the currently selected project appear in the Results list.

Project management functions are available from within the Sequence Manager, and are described in more detail in that chapter.

Selecting a Program

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To run an analysis, you simply click on the link to the specific program you want. SeqWeb can display the available Wisconsin Package programs in two ways, by Contents or Index. Depending on your familiarity with the Wisconsin Package, you may want to choose one way over the other. Click one of the buttons in the top left frame of the SeqWeb window to arrange the lower left frame according to your preference, as follows:

• Contents. If you are unfamiliar with the Wisconsin Package programs, you may want to choose Contents, which groups the programs by function. When you select a function in the lower left frame, the right frame displays the programs that fit that functional description. For example, the program function "Database Searching" groups programs such as BLAST, FastA, and ProfileSearch, which allow you to search peptide and nucleic acid databases with your own query sequence. Then, select the program you wish to run by clicking on its link in the frame on the right.

• Index. If you know the name of the program you want to run, you may want to choose Index, which lists the programs alphabetically. Select the program you wish to run by clicking on its link in the lower left frame.

Running a Program

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Before running a program, you should always check to make sure to select the appropriate project. The selected project determines which sequences appear in the program's Input Sequence list.

If you choose to run a program on a nucleic acid sequence, the Input Sequence list automatically displays only the nucleic acid sequences. Similarly, if you choose to run a program on a protein sequence, SeqWeb displays only the protein sequences.

When you run a program in SeqWeb, you must either wait for the program to complete before moving on to another program or loading a different web page or run the program in background.

To run a SeqWeb program:

1. Select a program.

   SeqWeb displays the program and its parameters. For online help regarding that program, click the book icon in the upper right corner.

2. From the Input Sequence list, select the sequence(s) you want to analyze.

   If the sequences you want to analyze do not appear in the Input Sequence list, consider the following:

   • Make sure the appropriate project is selected.

   • Add sequence(s) using the Local File, Clipboard, or Database buttons.

   • Use the Sequence Manager to ensure that the sequence you are looking for has the correct sequence type (protein or nucleotide).

   You cannot select sequences from two different projects; however, using the Sequence Manager's edit function, you can copy sequences from one project to another.

3. Review and adjust the parameters. (You may have to scroll to see all of the program parameters.)

   For online help regarding a specific parameter, click on the parameter name.

4. Click the Run button (or Run in Background) in the bottom frame. The program begins to run immediately.

   If you click Run, then the following occurs:

   • Depending on how quickly the program runs, you may see a clock at the bottom of the window that keeps track of how long the program is running.

     Note: Do not move to another website or click the browser's Back button before the program completes. These actions will cause SeqWeb to stop processing your job.

     When the program completes, SeqWeb displays the results. Through Preferences, you can set SeqWeb to display the results in the current window or to open a separate window to display the results.

   If you click Run in Background, the Job Manager window displays to keep you informed of the program's progress. After the program completes, click on View in the Job Manager window to see the program's results.

5. Save the results.

   See the Results Manager chapter for more information about analysis results.

You can run multiple SeqWeb programs simultaneously by opening additional browser windows and starting multiple SeqWeb sessions. However, the efficiency of this approach will depend on the sequences used, the programs run, and your system configuration.

Stopping a Program

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To stop a SeqWeb program that is currently running (not in background), click the Cancel button in the bottom frame.

To stop a SeqWeb program that is running in background, open the Job Manager and click the Cancel button.