TSSer

TSSer identifies transcription start sites (TSSs) genome-wide in bacterial genomes from differential RNA sequencing (dRNA-seq) data using a probabilistic framework to infer TSS positions for studies of bacterial transcription initiation and regulation.

Key Features:

• Probabilistic framework: Uses a probabilistic model to automatically infer TSSs from dRNA-seq signal.
• dRNA-seq analysis: Operates on differential RNA sequencing (dRNA-seq) datasets to detect transcription initiation sites.
• Genome-wide mapping: Performs genome-wide identification of TSSs in bacterial genomes.
• Enrichment detection: Identifies genomic positions preferentially enriched in dRNA-seq data.
• Capture-preference analysis: Detects positions preferentially captured relative to neighboring regions to refine TSS calls.
• Validation and discovery: Demonstrates high consistency with curated TSS lists and uncovers additional TSSs using publicly available datasets.
• Automated inference: Automates the computational inference of TSSs from sequencing data.

Scientific Applications:

• Genome-wide TSS annotation: Generate comprehensive TSS maps for bacterial genomes from dRNA-seq data.
• Transcriptional regulatory network analysis: Provide TSS locations to support studies of bacterial gene regulation and promoter architecture.
• Comparative and validation studies: Compare inferred TSSs with curated lists and publicly available datasets to identify novel transcription start sites.

Methodology:

TSSer applies a probabilistic framework to dRNA-seq data to identify genomic positions that are preferentially enriched and preferentially captured relative to neighboring regions and compares results to publicly available datasets and curated TSS lists.