生物資訊作業1
http://140.118.155.153/~web/teach/bi2006.htm
Homework 1
1. Based on the data provided by Dayhoff's paper in 1978, please compute
(1) PAM 250 (confirming your computation)
(2) PAM 66, PAM 300
(3) Mutability (= the chance of seeing a mutation = 1- Pr (no mutations) ) for each of the above cases
(The probability of seeing a mutation in either 66, 250 or 300 times of PAM1's evolution period,
of course, the answers are not 66%, 250% or 300%, or 34%, 1-250%, 1-300%)
Data & references:
(i) “A Model of Evolutionary Change in Proteins”, M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt,
Atlas of Protein Sequence and Structure, Vol5, 1978
(ii) Dataset, the mutation matrix from Dayhoff's 1978 paper
(iii) A sample Matlab code for a function call.
The mutation matrix includes two data sets: one is the mutation matrix and the other is
the probability of each amino acid (Pa ).
Here is the data if you want to type it by yourself.
(Please note that the order provide here or in Dayhoff's paper is not the same with the order used in PAM250
which we saw in the class)
Mutation matrix
| A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | |
| A | ||||||||||||||||||||
| R | 30 | |||||||||||||||||||
| N | 109 | 17 | ||||||||||||||||||
| D | 154 | 0 | 532 | |||||||||||||||||
| C | 33 | 10 | 0 | 0 | ||||||||||||||||
| Q | 93 | 120 | 50 | 76 | 0 | |||||||||||||||
| E | 266 | 0 | 94 | 831 | 0 | 422 |
你可能會有興趣的文章：
限會員,要發表迴響,請先登入 個人小檔案
搜尋
輸入關鍵字：
文章分類
月曆 文章排行榜
精選文章 我推薦的文章  |
