FAQ
 
Table of Contents: Why do colors in alignments made by Multiple Align Show become misaligned when the output window is resized? If you are running Multiple Align Show in Netscape, resizing the output window can cause the highlighting to change position when colored backgrounds are used. This problem seems to result from a bug in Netscape. One way to avoid the problem is to change Return as web page to Return as HTML source (on the Multiple Align Show page). The HTML code that is returned can be incorporated into an HTML file and viewed in Netscape without resizing problems.

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.

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:

  1. Highlight some text at the start of the text block and press SHIFT.
  2. Scroll down to the end of the file.
  3. While still pressing SHIFT, click the end of the text block.