About JASPAR

JASPAR is a regularly maintained open-access database storing manually curated transcription factors (TF) binding profiles as position frequency matrices (PFMs). PFMs summarize occurrences of each nucleotide at each position in a set of observed TF-DNA interactions. PFMs can be transformed to probabilistic or energistic models to construct position weight matrices (PWMs) or position-specific scoring matrices (PSSMs), which can be used to scan any DNA sequence to predict TF binding sites (TFBSs). The JASPAR database provides TFBSs predicted using the profiles in the CORE collection.

The motifs in JASPAR are collected in two ways:

• Internally: de novo generated motifs, by analyzing ChIP-seq/-exo sequences using a custom motif discovery pipeline (check the code at our repository).
• Externally: motifs taken directly from other publications and/or resources.

In both cases, the selected motifs are manually curated. Specifically, our curators assess the quality of the motif and search for an orthogonal publication providing support to the motif as the bona fide motif recognized by the TF of interest (e.g., a motif found in ChIP-seq peaks looks similar to one found by SELEX-seq). The Pubmed ID associated with the orthogonal support is provided in the TF profile metadata.

JASPAR is the only database with this scope where the data can be used with no restrictions (open source). For a comprehensive review of models and how they can be used, please see the following reviews

• Modeling the specificity of protein-DNA interactions Quant Biol. 2013 Jun;1(2):115-130
• Applied bioinformatics for the identification of regulatory elements Nat Rev Genet. 2004 Apr;5(4):276-87