Home ] Description ] [ Instructions ] Source Code ] Samples ] Applet ]

 

Instructions for using SequenceShop 1.0b:

1) GLOBAL alignment uses the following parameters:

Gap opening penalty: 1.2
Gap extension penalty: 0.6
Mismatch penalty: 0
Match score: 1

2) LOCAL alignment uses the following parameters:

Gap opening penalty: 1.2
Gap extension penalty: 0.6
Mismatch penalty: -0.6
Match score: 1

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
    within each Sequence entry field

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:

SequenceShop.class
Matrix.class
SSListener.class
SSInputsListener.class
SSItemListener.class

4) This program cannot be run from UNIX. It must be incorporated within a Web page
    using the following HTML code:

<APPLET CODE="SequenceShop.class" WIDTH=450 HEIGHT=600>
</APPLET> 
                               

5) All of the listed class files must be copied to the same directory as the displaying
    Web page

6) The applet works with Netscape Communicator browser version 4.5 and above (or any
     browser that supports JAVA 1.2)

7) The whole project can best be viewed by following this link: http://pantheon.yale.edu/~mjr33