funMotifs is a web-based tool designed for annotating noncoding variants and genomic regions
We have collected ChIP-seq, DNase-I, and other assays from ENCODE, FANTOM, RoadMap epigenomics and other data sources. We have used the data to annotate motifs of 510 transcription factors in 14 tissue types.
You can upload a list of variants or genomic coordinates and the tool will report the overlapping TF motifs and their annotations in a selected tissue type. A typical use-case is to annotate mutations from a certain cancer type with annotations from a corresponding tissue type. In order to summarize the annotations, we have applied a logistic regression model that enables prioritization of the variants and motifs.
The tool is open source and the pipeline is implemented in Python (source on GitHub). PostgreSQL is used to store and index the data that allows for very quick annotation retrieval.
The pipeline allows for re-generation of the annotations on a local computer to annotate larger sets of variants using a programming interface. Your comments and suggestions are appreciated.
Here is a link to the website: http://bioinf.icm.uu.se/funmotifs/