Using SynPlot to display the results of TFBSsearch.

Introduction.

TFBSsearch will produce a list of putative transcription factor binding sites in the GFF format. By default these relate to the first sequence of your global alignment. This information can be easily combined with the GFF files used to run SynPlot with the same global alignment. The SynPlot configuration file recognises the GFF <feature> 'CNS' and will plot each of the transcription factor binding site locations. Below is a brief tutorial for prodcing the final plot.

Tutorial.

  1. You must decide whether you need to mask out regions of your global alignment. Typically it is recommended you at least mask coding exon sequence and repeat sequences. You will need to prepare GFF files containing the features you wish to mask. Alternatively your global alignment may already be masked, in which case you do not need to mask again.
  2. You will need to input a representation of the transcription factor binding site, either as IUPAC code or nucleotide weight matrix. For this example we use a prepared file containing four codes for GATA, ETS, CEBP and homeobox sites.
  3. TFBSsearch can be run using the default settings. For the output to be compatible with SynPlot the numbers must be based upon the unaligned sequence (where gaps '-' are ignored).
  4. Using your favourite text editor you can copy the output and paste it into the your GFF files containing all the features you wish to view. By default your should be able to see vertical green lines representing your newly added data. Click on BEFORE and AFTER to see the addition of these transcription factor sites to the SCL locus.
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Last modified: Wednesday 9 April 2003.