F-seq

F-seq estimates continuous tag sequence density from high-throughput sequencing data to identify sequence features such as transcription factor binding sites from ChIP-seq and regions of open chromatin from DNase-seq.

Key Features:

• Continuous Tag Sequence Density Estimation: Generates a continuous representation of tag sequences to estimate tag density across the genome for improved feature resolution.
• UCSC Genome Browser Compatibility: Produces output compatible with the UCSC Genome Browser for genomic visualization.
• Java Implementation: Implemented in Java to enable cross-platform execution.

Scientific Applications:

• Transcription Factor Binding Site Identification: Identification and analysis of transcription factor binding sites using ChIP-seq data.
• Open Chromatin Region Analysis: Identification and analysis of regions of open chromatin using DNase-seq data.

Methodology:

Processes tag sequences from high-throughput sequencing (ChIP-seq, DNase-seq) to compute a continuous tag sequence density estimation.