Difference between revisions of "CSC334 Lab8"
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=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.'' | ||
| + | |||
| + | =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= | =Logos on the Web= | ||
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<br / > | <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: | 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]] | [[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: | ||
| + | |||
| + | 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 | ||
| + | |||
| + | |||
| + | Why is the information reported larger than 2.0? | ||
| + | |||
Revision as of 18:02, 4 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" />
Contents
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:
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
Why is the information reported larger than 2.0?
