Assignment 2: Due on Tuesday, October 7, by 11:59 PM
Note: Solution to the programming questions should be emailed to the instructor. See below for
how to create a subdirectory for each problem in the assignment. Your em ail should contain the
location of these sub-directories on the csil systems.
Note: See the course web page for the late turn-in policy. Also note that you may request a 3-day
extension at most once in the semester, by informing the instructor by e-mail.
Note: Collabor ation policy for
this
assignment – you may discuss the assignment with at most one
other student. See “Basic Information” link on the course web page for more details. (In shor t, you
may discuss, but must
do
the assignment on your own.)
1.
Local alignment with affine gap penalty
(30 points). Your task is to implement a dynamic
programming algorithm that finds the optimal local alignment of two input DNA sequences,
with affine gap penalty. The pro gram should take as input:
a. Two “Fasta” format files, each with one DNA sequence (format description as per previous
assignment).
b. A text file containing a 4 x 4 matrix of substitution scores, to be used in the alignment (see
sample below)
c. Two (non-positive) real numbers representing the “gap open” and “gap extend”
parameters.
The program will be run from the Linux comm and-line as:
<programfilename> <fastafilename1> <fastafilename2> <substitutionmatrixfile> <gopen>
<gextent>
The output of the program should be a textual display of the optimal local alignment (any one,
if more than one optimal solutions exist). In particular:
a. First, there should be a statement of the for m: “The optimal local alignment between given
sequences has score X and extends from position ? to position ? in sequence (name) and from
position ? to position ? in sequence (name).
b. Next, the alignment should be output in the following format:
A C C C - - A C - - A T - A . . . A T
A C - C G G A C A T A T T A . . . A T
G C C C - - G C - - G T - G . . . G T
G C - C G G G C G T G T T G . . . G T
