Difference between revisions of "CSC334 Lab8"

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[[Csc334_Labs | Back to lab page]]
 
[[Csc334_Labs | Back to lab page]]
 
<hr />
 
<hr />
 +
=Sequence Logos on the Web=
 +
[[Image:WebLogoOutput.png | thumb | 200px ]]
 +
<br />
  
−
=Introduction=
+
==Introduction==
 
This lab should be done in conjunction with [[CSC334_lab7 | Lab 7]] dealing with DNA sequence logos.  Please refer to the introduction section of  [[CSC334_lab7 | Lab 7]] for more information on ''sequence logos.''
 
This lab should be done in conjunction with [[CSC334_lab7 | Lab 7]] dealing with DNA sequence logos.  Please refer to the introduction section of  [[CSC334_lab7 | Lab 7]] for more information on ''sequence logos.''
  
−
=Logos on the Web=
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==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===
  
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==Input==
 
 
Point your browser to [http://weblogo.berkeley.edu  weblogo.berkeley.edu], which is one of the currently better logo generators on the Web.
 
Point your browser to [http://weblogo.berkeley.edu  weblogo.berkeley.edu], which is one of the currently better logo generators on the Web.
  
 
Enter the 8 sequences of  [[CSC334_lab7 | Lab 7]] in the input window, and click on the '''Create''' button:
 
Enter the 8 sequences of  [[CSC334_lab7 | Lab 7]] in the input window, and click on the '''Create''' button:
  
−
[[Image:WebLogoInputWindow.png]]
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[[Image:WebLogoInputWindow.png | thumb | 750 px | Input form of WebLogo Web site]]
  
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You should get something looking like this:
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Compare the output to the one you obtained in Lab 7.
  
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[[Image:WebLogoOutput.png]]
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<!-- [[Image:WebLogoOutput.png | thumb | 750px | Output of WebLogo ]] -->
  
 +
<br / >
 
   
 
   
 +
===Technical University of Denmark Logo Generator===
 +
 +
Another option is to point your browser to [http://www.cbs.dtu.dk/~gorodkin/appl/plogo.html www.cbs.dtu.dk/~gorodkin/appl/plogo.html], and to enter the same eight sequences, as illustrated below:
 +
 +
[[Image:cbsLogoInputWindow.png]]
 +
 +
Verify that you get the same logo as in the previous step.
 +
 +
You will notice that the logo output also gives the following results:
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 +
<code><pre>
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 +
Your data:
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 +
> CCCATTGTTCTC
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> TTTCTGGTTCTC
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> TCAATTGTTTAG
 +
> CTCATTGTTGTC
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> TCCATTGTTCTC
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> CCTATTGTTCTC
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> TCCATTGTTCGT
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> 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
 +
</pre></code>
 +
 +
==Questions==
 +
 +
# Why is the information reported larger than 2.0?
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# On the input page of the Technical University of Denmark, you will notice a line above an input box:
 +
 +
<code><pre>
 +
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
 +
</pre></code>
  
 +
::What do the the 0.05 numbers refer to?
  
  

Latest revision as of 17:02, 13 August 2008

<meta name="keywords" content="computer science, bioinformatics, DNA, CSC334, Lab" /> <meta name="description" content="DNA Sequence Logo Lab" /> <meta name="title" content="Bioinformatics Lab" /> <meta name="abstract" content="DNA Sequence Logo" /> <meta name="author" content="thiebaut at cs.smith.edu" />

Back to lab page

Sequence Logos on the Web

WebLogoOutput.png


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:

CbsLogoInputWindow.png

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?




Back to lab page

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