<your name + student ID>

• Write R or Python script to calculate the sum-of-pair score (SoP) of the multiple sequence alignment.
• Creating your own script with your student ID, ie. hw2_105753026.R.
• In this program, library Biostrings is only used to parse fasta file.

• hw2_ref.R: You can start from this reference code, and try to write your own comment in English
• pam100.txt
• pam250.txt
• test.fasta

• input: fasta file (ex. test.fasta)
• score: score file (ex. pam250.txt)
• gap: gap score

Executing your code with the following command.

Rscript hw2_studentID.R --input test.fasta --score pam250.txt --gap -10

python3 hw2_studentID.py --input test.fasta --score pam250.txt --gap -10

The answer is 999. You should print it on the screen.

10 testing data

Rscript hw2_studentID.R --input test.fasta --score pam250.txt --gap -10
Rscript hw2_studentID.R --input test2.fasta --score pam100.txt --gap -8
Rscript hw2_studentID.R --input data/test3.fasta --score pam/pam1.txt --gap -5

python3 hw2_studentID.py --input test.fasta --score pam250.txt --gap -10
python3 hw2_studentID.py --input test2.fasta --score pam100.txt --gap -8
python3 hw2_studentID.py --input data/test3.fasta --score pam/pam1.txt --gap -5

Correct answer gets 10 points of each testing data.

• High code similarity to others: YOUR SCORE = 0