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

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.


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.

Availability: 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatin Immunoprecipitation
  • Deoxyribonuclease I / chemistry
  • Deoxyribonuclease I / genetics
  • Genome
  • Sequence Analysis, DNA / methods*
  • Sequence Tagged Sites*
  • Software*


  • Deoxyribonuclease I