Hi,
it's been a
while since the first public release of
footprintDB, our database of DNA regulatory motifs and their cognate transcription factors with annotated interface residues. This resource can be reached at:
With help from
Álvaro Sebastián, who left the lab for a postdoc abroad, we have been updating it so that it currently contains
5,084 unique transcription factors,
7,685 position specific scoring matrices (
PSSMs) and
19,792 DNA binding sites, resulting from the integration of
17 motif collections, including our own
3D-footprint which is still used to annotate interface protein residues, those in direct contact with nitrogen bases of DNA.
The most recent news about footprintDB is its integration with
RSAT, the well known suite of tools for the analysis of regulatory sequences designed by the team of
Jacques van Helden. This means that all footprintDB motifs can now be used to annotate regulatory motifs using RSAT tools such as
compare-matrices.
Since we work mostly with plants, a subset of plant-related motifs is also available, which should fit the needs of researchers concerned with plant genomics. Indeed we are in charge of the plant RSAT mirror (
RSAT::Plants), which currently supports
41 plant genomes, with sequences and gene models obtained from
Ensembl Plants and
Phytozome.
We hope these new tools will be on interest to users,
Bruno
