Mostrando entradas con la etiqueta footprintdb. Mostrar todas las entradas
Mostrando entradas con la etiqueta footprintdb. Mostrar todas las entradas

8 de enero de 2024

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

7 de marzo de 2023

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:

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

 

Have a nice week,

Bruno