Contents:

• Collaboration Policy
• Overview
• Detailed Walkthrough
• Your Task
• Grading Standards

Collaboration Policy

For this assignment, you must work alone. Please make sure you adhere to the policies on academic integrity in this regard.

Topic: Sequence Alignment
Related Reading: class notes
Due:

This homework mirrors an earlier in-class exploration of an algorithm for computing the longest common subsequence, and other more advanced forms of sequence alignment. Specifically, we wish for you to compute alignments that optimize two metrics:

1. A simple alignment score (the so called Longest Common Subsequence) in which the metric is simply

   • +1 for a matched pair that are aligned

2. A scored alignment in which the metric includes

   • +1 for a matched pair that are aligned
   • -1 for a mismatched pair that are aligned
   • -1 for a character matched with an inserted gap in the opposite sequence

For a detailed explanation of the algorithms for computing these measures, and for a detailed walkthrough of an example alignment, see this attached description.

Your task is to anaylze a new pair of strings and to compute solutions for both the simple and advanced scoring functions (akin to what is given in the above detailed walkthrough). Specifically, for each of the two measures, you must do provide the following:

• Identify the maximum value of an alignment of the strings.

• Portray an alignment that achieves that optimal value. (That is, place one string immediately below the other, with gaps inserted to achieve the desired alignment.)

• Provide the entire table of scores that was used to compute the above results.

Your input strings: We have created a custom pair of strings for each student. To download YOUR individual data set, you must use your official SLUnet id (e.g. goldwamh), which is not to be confused with your SLU email address nor your Banner ID. The basic form of the URL to download your data set is http://cs.slu.edu/~goldwasser/1020/homeworks/align/input/username.txt except with your SLUnet username in place of username, using entirely lowercase letters. If you wish, enter your username into the form below (lowercased), and we'll take you directly to your data set.

This assignment is worth 40 points, which will be assessed with 20 points for simple metric (LCS) and 20 for the acvanced metric, broken down as

• (6 points)

  For correctly computing the value of the best alignment

• (6 points)

  For correctly portraying an actual alignment achieving the optimal score

• (8 points)

  For providing the full table that you used to compute the results.