F-Seq: a feature density estimator for high-throughput sequence tags.

Abstract

Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser. The software is written in the Java language and is available on all major computing platforms for download at http://www.genome.duke.edu/labs/furey/software/fseq.