Chapter 3. The Sequence Manager

Overview

What is the Sequence Manager?

Where can I find it?

Loading Sequences into SeqWeb

Sequence Formats Accepted

Adding Personal Sequences

Adding a Local Sequence File

Copying and Pasting Sequences from the Clipboard

Adding Database Sequences

Sequence Databases Available

Loading Database Sequences

Creating a New Sequence

Editing and Documenting Sequences

Renaming a Sequence

Editing Sequences

Copying Sequences

Viewing Sequences

Deleting Sequences

Saving Sequences

The Sequence Manager lets you load and manage sequences in SeqWeb. From the Sequence Manager you can load new sequences into SeqWeb as well as create, edit and document, copy, view, delete, and save sequences.

Where can I find it?

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Click on Sequence Manager in the bottom SeqWeb frame. The Sequence Manager page loads.

Loading Sequences into SeqWeb

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Note If you have sequence files you used in SeqLab or the command-line version of the Wisconsin Package, and you want to use them with SeqWeb, see "Transferring Sequences for Use in SeqWeb" in Appendix A, For SeqLab and Command-Line Wisconsin Package Users.

Sequence Formats Accepted

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SeqWeb accepts most GCG sequence file formats:

single sequence files in GCG format
multiple sequence format (MSF) files
rich sequence format (RSF) files

Note SeqWeb reformats MSF and RSF files and creates single sequences files out of the multiple sequences they contain. Note that SeqWeb does not accept list file format.

SeqWeb also accepts the following non-GCG sequence formats:

FastA
EMBL
GenBank
NCBI report format
IntelliGenetics
Staden

Adding Personal Sequences

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You can add personal sequences to SeqWeb in two ways: 1) you can specify a local file on your personal computer and upload it to the SeqWeb server, or 2) you can copy and paste a sequence into SeqWeb.

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.

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.
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...
    
    The File Upload dialog box (Netscape) or Choose file dialog box (Internet Explorer) appears.
  2. Navigate the directories and select the sequence of interest.
    
    You can refine the list of files displayed using wildcards. For example, *.seq would display only those files in the current directory with an extension of ".seq." Typing ecoo* would display only those files whose names start with "ecoo."
  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.

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

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.

To copy and paste on a PC or Macintosh:
1. 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.
In the Add from Clipboard window, click OK.

Adding Database Sequences

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Sequence Databases Available

SeqWeb provides the following DNA and protein databases. Because the databases are site configurable, your system administrator may have provided different databases than those listed below.

All DNA databases are a combination of sequences in GenBank and the EMBL Data Library. Due to the large duplication between GenBank and EMBL, GCG has eliminated EMBL sequence entries sharing the same primary accession number as sequences in GenBank.

**DNA Databases**
Name	Description
All DNA Databases	Includes all entries in GenBank and the abridged EMBL (GenEMBLPlus).
DNA Databases excluding EST and STS	Includes sequences from all divisions of both DNA databases except the EST and STS divisions (GenEMBL).
EST and STS	Includes only sequences from the EST and STS divisions of GenEMBLPlus (Tags).
Expressed Sequence Tags (EST)	Includes sequences derived from sampling cDNA libraries. Entries are mostly short and generated by automatic sequencing.
Genome Survey Sequences (GSS)	Includes short sequences from several genomes. Most entries have been generated by automatic sequencing.
Sequence Tagged Sites (STS)	Includes short, randomly primed regions of several genomes. The location of the entries make them important markers for genome mapping and sequencing.
Bacterial	Includes sequences derived from bacteria species.
High Throughput Genomes (HTG)	Include long, contiguous regions of several genomes usually at the cosmid level or longer. The entries are considered finished sequences.
Invertebrate	Includes sequences derived from invertebrate species.
Organelle	Includes sequences from mitochondria and other organelles. (EMBL only; GenBank entries are in the division of the host species).
Mammalian without Primate and Rodent	Includes sequences from all mammalian species except primates and rodents.
Vertebrate without Mammalian	Includes sequences from all vertebrate species except mammalian species.
Patent	Includes sequences submitted to the public databases by the European and United States Patent Offices.
Phage	Includes sequences from bacteriophage.
Plant	Includes sequences from plant, fungal, and algal species.
Primate	Includes sequences from primate species.
Rodent	Includes sequences from rodent species.
Structural RNA	Includes RNA sequences with solved structures. (Not all structural RNAs have a solved structure.)
Synthetic	Includes man-made sequences, mostly vectors, regions of vectors, or genetically engineered plasmids.
Unannotated	Includes entries which have incomplete documentation or other problems. Entries in this division will move to another division in a future database release.
Viral	Includes sequences from all viral species except bacteriaphage.

**Protein Databases**
Name	Description
SWISS-PROT	Includes all SWISS-PROT entries.
Translated EMBL	Includes most of the proposed translated regions of the complete EMBL except those regions with entries already in the SWISS-PROT database (SP-TREMBL).
SWISS-PROT plus Translated EMBL	Includes all SWISS-PROT and SP-TREMBL entries (SwissProtPlus).
PIR	Includes all PIR entries.

Loading Database Sequences

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

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.
Select the appropriate database from the Database selection menu.

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

SeqWeb displays sequence(s) with matching name(s).
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.
Click Add Selected.

The sequences are loaded into the Sequence Manager list.

See "Saving Results" in Chapter 4, Sequence, Text, and Graphic Results

Creating a New Sequence

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

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.

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.
In the Add from Clipboard window, click OK.

The sequence is loaded into the Sequence Manager list.

Editing and Documenting Sequences

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Note If you have the Project Manager enabled, SeqWeb displays only those sequences loaded in your currently selected project.

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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Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click Rename.

SeqWeb displays a list of your currently loaded sequences.
Select a sequence from the list.

The sequence's description displays in the status line at the bottom of the browser window.
Click the Rename button on the right of the sequence list.

The Rename window appears.
Type the new name of the sequence in the Name text box.
Click OK.

The renamed sequence appears in the sequence list.

Editing Sequences

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Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click Edit.

SeqWeb displays a list of your currently loaded sequences.
Select a sequence from the list.

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

Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click Copy.

SeqWeb displays a list of your currently loaded sequences.
Select a sequence from the list.

The sequence description displays in the status line at the bottom of the browser window.
Click the Copy button on the right of the sequence list.

The Copy window appears.
Type a new name for the sequence copy in the Name text box.
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.

Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click View.

SeqWeb displays a list of your currently loaded sequences.
Select a sequence from the list.

The sequence description displays in the status line at the bottom of the browser window.
Click the View button on the right of the sequence list.

The View window appears, displaying the contents of the sequence.
Click Close to close the View window.

Deleting Sequences

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Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click Delete.

SeqWeb displays a list of your currently loaded sequences.
Select one or more sequences.

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

Saving Sequences

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SeqWeb automatically saves those sequences you have loaded on the server. However, to ensure that sequences of interest are not lost, you may want to save them to your local computer. SeqWeb saves these sequences to your local computer as GCG-formatted text files.

Netscape and Internet Explorer behave differently in saving files. Choose the appropriate browser below.

See "Saving Results" in Chapter 4, Sequence, Text, and Graphic Results

"Saving Results from the Results Manager to Your Local Computer" in Chapter 6, The Results Manager

To save sequences:

Select Sequence Manager.

The Sequence Manager page loads.
Under Sequence Manager Functions, click Save As.

SeqWeb displays a list of your currently loaded sequences.
Follow the steps for the web browser you are using:
- Netscape
  1. Select one or more sequences.
  2. Click Save As... An Unknown File Type dialog box appears.
  3. Click Save File... A Save As... dialog box appears.
  4. Confirm the directory location and filename for saving the results and click OK.
    
    SeqWeb displays an Unknown File Type dialog box and a Save As... dialog box for each sequence you selected.
- Internet Explorer
  1. Select one sequence and click Save As... A File Download dialog box appears.
  2. In response to the What would you like to do with this file? prompt, click Save this file to disk.
  3. Click OK. A Save As dialog box appears.
  4. Confirm the directory location and filename for saving the results and click Save.
  5. Repeat steps a - d for each sequence file you want to save.
    
    The file(s) are saved to the directory you specify.

Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com

Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.

All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.