Each question, by default, should be solved INDIVIDUALLY, unless marked as \collaborative". Questions marked as \collaborative" implies that for those questions you are encouraged (but not required) to discuss with other students. There is no limit imposed on how many of your class students can collaborate on such questions, as long as you acknowledge the participants along with a brief statement about their contributions to those discussions, in the Cover Sheet provided (available on the course website and OSBLE). You are also welcome to use OSBLE to have an online discussion. Note, however, that none of these discussions can involve students or people from outside this class. As for the content, your discussion should be restricted to gain a better understanding of the problem/question better and to explore higher level approaches and ideas for solving the problem. Showing/sharing each other's solutions will be considered \cheating" and is strictly prohibited. The nal writing of your solution should be entirely yours.

Some thumbrules to make your discussions eective:

- If you think you have solved a problem, then please resist from posting/disclosing your key ideas to others. Instead, your role in a discussion should be to try and direct others to thinking about the same way as you did. This will encourage others to think and arrive at their solutions on their own, and even possibly come up with alternative ways of solving it.

a) Unless otherwise speci ed, sequences are over the DNA alphabet, Σ = { a; c; g; t }.

b) If s denotes a DNA sequence, its string reverse is denoted by s^r, and its reverse complement is denoted by s^rc.

c) Let |s| denote the length of s, and the i^th character in s be denoted by s[i]. Let s[i::j] denote the substring starting at i and ending at j in s.

d) Scoring scheme: Score for each match is m_a; mismatch is mi; and gap is g. For affine gap, use h for opening gap score and g for gap continuation score.