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ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available to extract binding motifs from peak data sets. However, most approaches are only available as command-line programs, or via a website but with size restrictions. We present peak-motifs, a computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genomedoi:10.1093/nar/gkr1104 pmid:22156162 pmcid:PMC3287167 fatcat:uxtmsfltwngohedr6ebpgbzm6e