Name: CHEN LIN Student ID: 44141569-3

11300A Bioinformatics
Homework 2 Nov. 18, 2014 1. Sequence Alignment Using Dynamic Programming (DP) There are two amino acid sequences, seq1: COELACANTH and seq2: PELICAN. Obtain the global alignment by using DP (the Needleman-Wunsch algorithm) .
$+ 1 for letter that match ! Scoring scheme : #- 1 for mismatches !- 1 for gaps " 

Answer: ————————————————————————— C O E L A C A N T H P E L I C A N ————————————————————————— -1 -1 1 1 -1 1 1 1 -1 -1 λ λ P E L I C A N
Seq1 Seq2

C -1 -1 -2 -3 -4 -3 -4 -5
O P

O -2 -2 -2 -3 -4 -4 -4 -5
E E

E -3 -3 -1 -2 -3 -4 -5 -5
L L

L -4 -4 -2 0 -1 -2 -3 -4
A I

A -5 -5 -3 -1 -1 -2 -1 -2
C C

C -6 -6 -4 -2 -2 0 -1 -2
A A

A -7 -7 -5 -3 -3 -1 1 0

N -8 -8 -6 -4 -4 -2 0 2
N N

T -9 -9 -7 -5 -5 -3 -1 1
T —

H -10 -10 -8 -6 -6 -4 -2 0
H —

0 -1 -2 -3 -4 -5 -6 -7
C —

Name: CHEN LIN Student ID: 44141569-3 Seq1 Seq2 C P O — E E L L A I C C A A N N T — H —

2. In this question you will use two different dot matrix analysis servers to analyze the sequence of the human low density lipoprotein receptor (NP_000518). You will run a dot matrix analysis of this protein against itself (which means you will need to enter its sequence in both boxes on the website). A. First use Dottup (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::dottup). Set the word size to 2 (“word size” is basically the same as “window”). Using a word size of 2, the algorithm will scan a window of 2 amino acids and put one dot in the matrix when the two sequences have identical amino acids. Dottup has no threshold, so it is simpler than Dotmatcher. a) Print (or copy and paste) the output from Dottup and turn it in.

B. Now use Dotmatcher (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::dotmatcher). Set the window to 10 and threshold to 23 in order to filter out the “noise.”

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