Difference between revisions of "Promoter Analysis"
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==Setting up== | ==Setting up== | ||
# Load a set of nucleotide sequences of interest. | # Load a set of nucleotide sequences of interest. | ||
| − | # Go to the '''Promoter''' component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA- | + | # Go to the '''Promoter''' component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA-box:MA0108". |
| − | |||
| − | + | The motif is graphically depicted on the "Logo" tab: | |
| − | [[Image: | + | [[Image:T_Promoter_Logo_TBP.png]] |
The Parameters tab: | The Parameters tab: | ||
| − | [[Image: | + | [[/Image:T_Promoter_Parameters_initial.png]] |
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[[Image:T_Promoter_Sequence.png]] | [[Image:T_Promoter_Sequence.png]] | ||
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==Running and viewing the scan== | ==Running and viewing the scan== | ||
Revision as of 14:53, 12 October 2009
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Outline
In this tutorial, we will
- Select a transcription factor motif to scan against a set of sequences.
- Run the scan.
Overview
The Promoter Component allows a set of sequences to be scanned by selected motifs of known transcription factor binding sites. These motifs are derived from the Jasper project. The motifs are in the form of PSSM - Position Specific Scoring Matices.
The Promoter component will also display the results of hits found in the Pattern Discovery component.
It should be noted that in general, the discovery of functional transcription factor binding sites involves biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses.
Setting up
- Load a set of nucleotide sequences of interest.
- Go to the Promoter component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA-box:MA0108".
The motif is graphically depicted on the "Logo" tab:
The Parameters tab:
/Image:T_Promoter_Parameters_initial.png
The Sequence tab:
Running and viewing the scan
- Hit Scan.
- Check the box "Show TFs".
- Hits of this motif against the sequences are displayed in the sequence window.
