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Instructions for using SequenceShop 1.0b: 1) GLOBAL alignment uses the following parameters: Gap opening penalty: 1.2 2) LOCAL alignment uses the following parameters: Gap opening penalty: 1.2 3) Press the ENTER key after typing in every input and every time your change a field! 4) To restore case-sensitivity after an ALL-UPPERCASE alignment, ENTER must be pressed 5) "Score" = number of matches between sequences
Instructions for compiling SequenceShop under UNIX (Pantheon): 1) Copy SequenceShop.java (source code) into a UNIX directory 2) At the UNIX prompt type: javac SequenceShop.java 3) This will generate the following ".class" files in the same directory:
4) This program cannot be run from UNIX. It must be incorporated within a Web page <APPLET CODE="SequenceShop.class"
WIDTH=450 HEIGHT=600> 5) All of the listed class files must be copied to the same directory as the
displaying 6) The applet works with Netscape Communicator browser version 4.5 and above (or any 7) The whole project can best be viewed by following this link: http://pantheon.yale.edu/~mjr33 |