In this tutorial, we will attempt to predict cis-regulatory motifs for a set of genes of interest, based on the discovery of conserved motifs in the promoters of their orthologs (phylogenetic footprints). This aproach was proposed in the end of the 1990’s, when a few genomes only were available. With the ever-increasing speed and ever-decreasing costs of sequencing projects, the number of completely sequenced genomes follows an exponential growth, and the power of comparative genomics methods increases accordingly.
The anlaysis of phylogenetic footprints is particularly fruitful in small genomes (Bacteria, Fungi), where cis-regulatory elements are located in delimited regions circumscribed to a few hundred base pairs upstream of the transcription start site.
This tutorial assumes that you already learned the theory in the following chapters.
Chapter | Slides |
---|---|
Phylogenetic footprints - introduction | 03.4.2.comparative_genomics.pdf |
Discovering phylogenetic footprints in bacterial genomes | 03.4.3.footprint_discovery.pdf |
In a first time, we will identify the genomes in which your transcription factor of interest has a putative ortholog. We use a somewhat rudimentary (but pragmatic) approach to identify putative ortholog, by selecting the bidirectional best hits (BBH).
Note that the result page is currently resricted to a header, and the result table is empty. The process may take some time (3-4 minutes per gene), but you will already be able to consult the results after a few minutes, and then periodically refresh the result page to check the progress of your query.
While the first analysis is running, we can start the same analysis with one modified parameter:
The analysis with operon inference is somewhat slower, but the results are generally more relevant. You can now let run the analyses on the server, and periodically check the results of the two processes.
The interpretation of the results will be discussed during the course
TO BE DONE