JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, 
non-redundant transcription factor (TF) binding profiles representing 
transcription factor binding preferences as position frequency matrices for 
multiple species in six taxonomic groups. For this 2016 release, we expanded the 
JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 
in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 
profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent 
an 83% expansion and 10% update when compared to the previous release. We 
updated the structural annotation of the TF DNA binding domains (DBDs) following 
a published hierarchical structural classification. In addition, we introduced 
130 transcription factor flexible models trained on ChIP-seq data for 
vertebrates, which capture dinucleotide dependencies within TF binding sites. 
This new JASPAR release is accompanied by a new web tool to infer JASPAR TF 
binding profiles recognized by a given TF protein sequence. Moreover, we provide 
the users with a Ruby module complementing the JASPAR API to ease programmatic 
access and use of the JASPAR collection of profiles. Finally, we provide the 
JASPAR2016 R/Bioconductor data package with the data of this release.