Table of Contents: Why don't Multiple Align Show alignments print properly when colored backgrounds are used? HTML tables are used to add background coloring to letters when the colored backgrounds option is used in Multiple Align Show. Some Internet Explorer versions have an option to allow colored backgrounds to be printed. For example, with Internet Explorer 5.5 (Windows) you can allow backgrounds to be printed by doing the following:
  • Choose Internet Options from the Tools menu.
  • Click the Advanced tab in the dialog box that opens.
  • Under the Printing category check Print background colors and images.
  • Click OK.
In many versions of Netscape Communicator you can print backgrounds as follows:
  • Choose Page Setup from the File menu.
  • In the Page Options section check Print backgrounds.
  • Click OK.
Another way to print alignments is to generate a PDF using Acrobat Distiller. This technique has been used on the Macintosh using Netscape Communicator 4.6 (thanks to Russell Reagan for this information):
  • Choose Page Setup from the File menu.
  • In the Page Options section check Print backgrounds.
  • Click OK.
  • Choose Print from the File menu.
  • Check Print to file in the Print dialog box.
  • Click OK.
  • Use Acrobat Distiller to convert the postscript file to a PDF.
  • The PDF can be modified using Adobe Illustrator. For example, you can add asterisks and bars to highlight portions of interest in the alignment.
The best way to print alignments if your browser does not print the colored backgrounds is to first take a screen shot.

Why aren't results appended to existing data in the output window? The original version of the Sequence Manipulation Suite appended new results to existing data in the output window. This approach caused problems on some platforms, and made printing and saving results difficult. For these reasons existing output data is now replaced when new output data is generated.

When I select and copy data in the output window and then close the output window the data cannot be pasted. Depending on the browser type and version you are using, you may need to keep the output window open when copying and pasting data between the output window and other applications.

Which web browsers can run the Sequence Manipulation Suite? All the scripts have been tested in Internet Explorer 4.0 and 5.0 (Windows), Netscape Communicator 4.6 (Windows), Internet Explorer 4.5 (Mac), Netscape Communicator 4.6 (Mac), and Netscape Communicator 4.6 (Linux).

Why do some programs take a long time to finish? The time needed for the applications to complete their tasks depends on the web browser you are using and how much input you give them. Try short sequences first to gauge how they perform on your computer.

How do I save the contents of the output window? If you are using Netscape select Save As from the File menu. Enter a file name and select HTML Files from the Save as type list and click Save (the procedure may differ slightly between Netscape versions). If you are using Internet Explorer select Save As from the File menu. Enter a file name and select Web Page HTML only from the Save as type list. Click Save to save the file (the procedure may differ slightly between Internet Explorer versions).

Can I run the Sequence Manipulation Suite off-line? You can download a zipped version of this site if you wish to use it off-line.

What does it mean when GenBank Feature Extractor/GenBank Trans Extractor/GenBank to FASTA says the entire GenBank file may not have been processed? The Sequence Manipulation Suite programs that accept GenBank files generate a warning if the // symbol is missing from the file, since its absence suggests that some of the sequence may be missing.

Why is there a limit to the amount of text that can be entered into a text area? Some web browsers limit the amount of text that can be entered into a text area. Once this limit is reached, additional text is not displayed in the text area, and it is not made available to programs that access the text area. You may want to try a different web browser if you find that the one you are using has a low input limit for text areas. For example, Internet Explorer 5.0 for Windows accepts much more input than Netscape Communicator 4.7 for Windows. Netscape Communicator 4.6 (Mac) accepts much more input than Internet Explorer 4.5 (Mac).

Which degenerate base characters can be included in a DNA sequence? The only degenerate base that is accepted is n. If you want to use a sequence that contains other degenerate characters first use Filter DNA to convert those characters to n's.

Which amino acid characters are accepted? The standard IUPAC characters are accepted by the programs that handle protein sequences. Gaps (. and -) and X are accepted by the programs that handle multiple alignments. Z and * are accepted by the programs that reverse translate proteins (they are interpreted as stops).

How can I take a screen shot of the output of Multiple Align Show? On most Windows platforms you can press ALT + PRINT SCREEN to copy a picture of the active window to the Clipboard. The contents of the Clipboard can then be pasted into a graphics program for editing, saving, and printing. On the Mac, pressing SHIFT + Apple + 3 will save a picture of the screen to a file named Picture1, Picture2, etc.

Is there a fast way to select large blocks of text? The best way to select a large block of text, such as the contents of a GenBank file, is as follows:

  • Highlight some text at the start of the text block and press SHIFT.
  • Scroll down to the end of the file.
  • While still pressing SHIFT, click the end of the text block.
How do I run COMBOSA scripts in RasMol? On Windows platforms copy the script and paste it into a text editor. Save the script as a text file (so that it has the .txt extension), and place it in the same folder as RasMol. Load the molecule you wish to examine into RasMol, then type script followed by the name of your text file (include the .txt extension) into the RasMol Command Line window and press enter. For more information on using RasMol see the RasMol manual.

How can I make sequence alignments that can be formatted by Multiple Align Show? You can use a variety of programs to align sequences so that they can be used by Multiple Align Show (and COMBOSA and Multi Rev Trans). The BCM search launcher provides Web access to ClustalW and other programs that will align sequences and return them in FASTA format. The Canadian Bioinformatics Resource also provides ClustalW access (select GDE as the output format). Another option is to download and use ClustalW on your own computer as ClustalX.

How can I edit the output produced by the Sequence Manipulation Suite?  If you are using Netscape, you can easily make changes to the output produced by most programs in the Sequence Manipulation Suite. When output is shown in the output window, select Save As from the File menu. Enter a file name, and choose HTML files from the Save as type list. Next, select Open Page from the File menu. In the dialog box that opens, click Choose File, and navigate to the file you just saved. Once the file is loaded into Netscape, select Edit Page from the File menu. Now you can edit the file and save the changes or print the results. Note that this procedure may differ slightly depending on the Netscape version and platform you are using.