Help in Bioinformatic

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I have a Bioinformatic assignment, my doctor gave us a code in Ruby language. This code is to do a global alignment, and the doctor wants semi-global alignment. So we have to modify the code of global alignment to be semi-global alignment. I will attached the code for you. Second add numbers to make longer alignments more readable
 
That what I want
 
I attached Five files.
 
1. The code of global alignment with the output to use it to make the change on it to be semi global alignment.
 
2. I attached the question file that has the two questions with details
 
3. It has class-note link (Here is doctor’s explanations, examples, etc…) This assignment is number 3. So when you open the class-note link, make sure that you look at assignment 3 because this link represent the whole chapters, and Assignment 3 start from:
 
Chapter 3 St. Clair & Visick, continued
Tuesday, October 21 to Thursday, October 30 
 
4. chapter 3 from the book.
 
5. Data used in homework assignment 3
 
feel free to contact me at 2026602607.
 
Please this assignment is very important to me if you don’t know how to do it let me know, please do not try to do it if 100% that you do it.

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