Venue: Biomedicum 1 Seminar room 3

Timing: 15:30 onwards

Presenter: Jarkko Toivonen

MODER: discovering structures of dimeric transcription factor binding sites

Transcription factor (TF) binding sites can be modeled with the usual
Position-specific Probability Matrices (PPMs).
However, when using these models to scan the genome, too many
putative binding sites are predicted. This binding site discovery
can be alleviated by incorporating additional information
about the binding process. One source of additional information
is the collaborative binding of TFs. To obtain information
of collaborative binding we have developed an algorithm
and a program called MODER, which learns a total probability model
which includes monomeric models for binding sites and for
their dimeric interactions.

In this talk I will first briefly introduce the problem MODER
solves. After that I will show examples of running MODER and
introduce the visualization of the results.

MODER is freely available at:
https://github.com/jttoivon/moder

For more reading:
https://doi.org/10.1093/nar/gky027