footprintDB January 2025 version

Hi, we just updated the motifs, transcription factors and sites in the database footprintDB. 

The January 2025 version adds:

1)  Motifs inferred from  protein-DNA complexes at the Protein Data Bank, added to 3d-footprint by  19/12/2024; note the complexes are also used to annotate interface residues  of all transcription factors (TFs).

2) New plant data at EEADannot, with TFs assigned to Plant-TFClass families (see repo).

The current contents include:

	total	unique	metazoa	plants
Transcription Factors	9976	7322	4839	1256
DNA motifs (PSSM)	17117	14828	8893	2962
DNA Binding Sites/Sequences	68358

The footprintDB motifs have also been synced with RSAT (see repo), see you soon,

Bruno

footprintDB added new TFs, cis elements and binding interfaces

Over the last couple of weeks I have carried out the annual update of footprintDB, our database of transcription factors (TFs) with annotated cis elements and binding interfaces.

This involved three consecutive steps:

1) Updated 3d-footprint (completed 21/12/2023). This means that the collection of protein-DNA complexes from the Protein Data bank was updated and will help annotate more interface residues in TFs.

2) Updated the EEADannot collection with plant motifs and sites manually curated by us from papers published recently. You can see the sources at https://github.com/eead-csic-compbio/EEADannot .

3) Added JASPAR 2024 data and predicted interface residues for all included TFs.

 

You can check the current contents of each collection at https://footprintdb.eead.csic.es/index.php?databases , an overall summary is shown here:

 

The data can be downloaded in FASTA and TRANSFAC formats at https://footprintdb.eead.csic.es/download and the motifs have also been updated in https://github.com/rsa-tools/motif_databases , which feeds RSAT servers (see the plants server here). Note that some collections were left out due to licensing limitations.

Bruno

footprintDB moved to a new server

Dear all,

shortly after the changes reported on Twitter, our server footprintDB, first published in 2014, has moved to a new server.

The new URL is https://footprintdb.eead.csic.es and accesses to the old site [http://floresta.eead.csic.es/footprintdb] will be redirected here. 

Here's a summary of updates:

• A new release of the EEADannot collection was produced.
  
• Downloadable data are now CC-BY-NC-SA license, leaving out RegulonDB.
• The new server supports certbot HTTPS, runs mariadb instead of mysql, and deprecates the SOAP Web Services interface, and its client (https://github.com/eead-csic-compbio/footprintDBclient).
• The plant contents currently include 1233 transcription factors and 2252 DNA motifs.
  

Motif of BIL1/BZR1, https://footprintdb.eead.csic.es/index.php?db:EEADannot&motif=BZR1.

 

Have a nice week,

Bruno