Dynamic Programming: String Alignment

The exercises of this week are about string alignments.

Task 1

Work through the biorecipe about Dynamic Programming. When you are finished, you should understand the algorithm for global alignments, as well as the corresponding Darwin code. As long as anything remains unclear, better ask one of the assistants.

Task 2

Modify the code of the bio-recipe to make the alignments local instead of global. The difference between local and global alignments is described in Section 8.3.6 (pp. 140/141) of the script.

Some tips on working with Darwin: Darwin is an interactive language, you can simply execute commands by typing them into the command prompt. When writing a longer program (like here), however, it is a good idea to write the program in an editor and then piping the file directly into Darwin:

darwin < myCode.txt

or copy/pasting the code to Darwin. This makes it easier to correct any mistakes/bugs in the program, without having to retype the whole code. Also, this helps to keep an overview of the whole program.