CSC334 Lab8

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Introduction

This lab should be done in conjunction with Lab 7 dealing with DNA sequence logos. Please refer to the introduction section of Lab 7 for more information on sequence logos.

Play sequences

We are going to use the following sequences in this lab, but feel free to use your own sequences

CCCATTGTTCTC
TTTCTGGTTCTC
TCAATTGTTTAG
CTCATTGTTGTC
TCCATTGTTCTC
CCTATTGTTCTC
TCCATTGTTCGT
CCAATTGTTTTG

Logos on the Web

Berkeley Logo Generator

Point your browser to weblogo.berkeley.edu, which is one of the currently better logo generators on the Web.

Enter the 8 sequences of Lab 7 in the input window, and click on the Create button:

Input form of WebLogo Web site

Compare the output to the one you obtained in Lab 7.

Technical University of Denmark Logo Generator

Another option is to point your browser to www.cbs.dtu.dk/~gorodkin/appl/plogo.html, and to enter the same eight sequences, as illustrated below:

Verify that you get the same logo as in the previous step.

You will notice that the logo output also gives the following results:

 Your data:

 > CCCATTGTTCTC 
 > TTTCTGGTTCTC 
 > TCAATTGTTTAG
 > CTCATTGTTGTC
 > TCCATTGTTCTC
 > CCTATTGTTCTC
 > TCCATTGTTCGT
 > CCAATTGTTTTG

 Your amino acid distribution:

 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
 The distribution of information over the alignment:

 position information/entropy
    1       3.3219
    2       3.5106
    3       2.8219
    4       3.7784
    5       4.3219
    6       3.7784
    7       4.3219
    8       4.3219
    9       4.3219
   10       3.0231
   11       3.2606
   12       3.0231

 Information content for the whole alignment: 43.8059

Questions

1. Why is the information reported larger than 2.0?
2. On the input page of the Technical University of Denmark, you will notice a line above an input box:

A priori amino acid distribution (4 decimal precision):
pA; pC; pD; pE; pF; pG; pH; pI; pK; pL; pM; pN; pP; pQ; pR; pS; pT; pV; pW; pY;
0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 

What do the the 0.05 numbers refer to?

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