CS 368 Bioinformatics Homework 1 (2/11/2025) PDF

CS 368 Introduction to Bioinformatics Homework 1 (Submit to D2L Assignments by 11:00PM 2/11/2025) All answers and solutions should be typed. Scanned handwritings will not be accepted. The solution (except some amino acid sequences for Problem 1 and the tables for Problems 2 and 3) o...

CS 368 Introduction to Bioinformatics Homework 1 (Submit to D2L Assignments by 11:00PM 2/11/2025) All answers and solutions should be typed. Scanned handwritings will not be accepted. The solution (except some amino acid sequences for Problem 1 and the tables for Problems 2 and 3) of an older version is posted as a reference. You may use the online Freiburg RNA Tools to solve problems 2 and 3. Submit one single document with tables and images in it. Do not submit multiple files or a zip file of multiple files. Total: 40 Points 1. (12pts) (Suppose the DNA sequence in this problem is part of an exon.) (a) Find the six reading frames that can be obtained from the DNA sequence 5'- CGGTACTGAGCTG-3'. Give the answers 5' to 3'. (b) List the amino acid sequences translated from the six reading frames. 2. (9pts) Global sequence alignment a) Using the Needleman and Wunsch dynamic programming method, construct the partial alignment score table for the following two sequences, using the following scoring parameters: match score = +3, mismatch score = +1, linear gap penalty = 1 (i.e., gap score = -1). Sequence 1: TGATAGC Sequence 2: GATGCT Show the table. b) Use the table to find an optimal global sequence alignment. Show the alignment. c) What is the score of the optimal global sequence alignment? 3. (9pts) Local sequence alignment a) Using the Smith-Waterman method, construct the partial alignment score table for a local alignment of the following two sequences, using the following scoring parameters: match score = +1, mismatch score = -1, linear gap penalty = 2 (i.e., gap score = -2). Sequence 1: TGATAGC Sequence 2: GATGCT Show the table. b) Use the table to find an optimal local sequence alignment. Show the alignment. c) What is the score of the optimal local sequence alignment? 4. (10pts) Dot Plots Construct the dot plot for the two sequences TGAATATC and TGCATATC using the following two different approaches. a) Use the simple technique, i.e., place a dot in the plot for each identical pair of nucleotides. b) Use a sliding window of size 3 and a mismatch allowance of 1 nucleotide.