Molecular Toolkit Help

Almost all of the programs require input of nucleic acid or amino acid sequences into a text box. You can enter such sequences manually, but usually you will copy a sequence from another source and paste it into the text box. To copy text on Windows platforms, simply select the sequence (e.g. from a web page, word processor or text editor) by dragging your mouse across that text, then copy it to the clipboard using Ctrl-C. Next, click on the sequence entry text box in the program you are using, and paste in from the clipboard by pressing Ctrl-V. If you are using a MacIntosh, hold down the [Apple] key (%) and press C for copy or V for paste.

All characters in the text you enter are converted to upper case and the sequence is extracted according to the following rules:

• Nucleic acids - All characters except A,C,T,G,U (standard nucleotide codes) and N,R,W,Y,M,K,S,H,B,V,D (ambiguous nucleotide codes - see below) are ignored. All U's are converted to T's, and all ambiguous codes are converted to N's.
• Peptides - Input data must be in the form of single character codes for amino acids (see below). Additionally, the '-' character is interpreted as a stop codon, and the 'X' character as an unknown amino acid. All other characters are ignored.

Thus, all numbers and whitespace that you paste into sequence input boxes is ignored, which makes it easy to copy from Genbank or EMBL database entries. However, be cautious about including extraneous text, which may be misinterpreted as legitimate sequence data.

Java applets displayed on a web page cannot be directly printed (you'll get a large blank area on the output). However, in all of these programs, text output is placed in text boxes, and the text can be selected, copied to the clipboard, then pasted into a text editor or word processor.

At this time, graphical output cannot be directly printed. When time permits, I'll write the code to convert Java images into gif files for display and printing. However, graphical images in applets displayed in a browser can be easily copied and transferred into other programs for printing:

• Windows 95/NT: Hold down ALT key and press Print Screen key to copy the currently active window (e.g. your browser) to the clipboard. You can then open the Paint program (or most word processors or graphics programs) and paste the captured image into it for cropping, printing, etc.
  
  
• Macintosh: Hold down the [Apple key] and the Shift key, and press the [3 key] - an image of the screen will be captured and either put on your desktop or written to disk as "Picture x" for use in other programs.
  
  
• X Windows systems: Use a program like xv to perform a screen capture.