tammykan / nccubio Goto Github PK

hw1 : generate PAM250 from PAM1
write R script to generate PAM250 from PAM1

1. install R & RStudio on your computer
2. test R in commend mode by Rscript hw1.R, and you should get
3. write your own R script, hw1_.R , ie. hw1_0936268888.R,
   to read pam1.txt and output pam250.txt
4. create Github account and make a new repository, nccubio.
5. make a folder hw1
6. upload your local R script into your GitHub hw1 folder
7. paste your GitHub path on this assignment

References:
You can start from hw1_ref.R.
Please refer to week3_github.pptx about how to use R and GitHub.

pro2 : pairwise alignment
write R script to perform pairwise alignment

•Parameters
linput test.fasta
lscore pam250.txt
laln global|local
lgap_open
lgap_extend
loutput result.fasta
•Commend
–Rscript hw2_.R --input test.fsta --score pam250.txt --aln global --gap_open -10 --gap_extend -2 --output result.fasta
hw2_.R
i.e., hw2_0936268888.R
Upload your code to under folder, hw2, in your nccubio GitHub.
i.e., https://github.com//nccubio/hw2
Score evaluation

•80: global alignment
•85: matrix
•90: local alignment
•95: two gap-penalty scheme
–gap open
–gap extend
References:

You can start from pro2_ref.R.