PositionScan

PositionScan is a computational tool designed to identify specific patterns within biological sequences, such as DNA, RNA, or proteins. Developed by a consortium of bioinformatics researchers, the program implements a sliding‑window algorithm that scans input sequences for motifs that meet user‑defined criteria. The software supports both exact pattern matching and degenerate motif recognition, allowing users to specify IUPAC nucleotide codes or regular expressions. PositionScan can be executed from the command line and accepts input files in FASTA or GenBank format. Results are output as tabular summaries indicating motif positions, orientation, and frequency, and can be further processed with downstream tools for enrichment analysis or visualisation.

Key features include multithreading support for large genomic datasets, a hierarchical motif hierarchy that enables nested pattern detection, and an integrated reporting system that generates summary statistics and sequence logos. PositionScan has been cited in multiple studies examining transcription factor binding sites, microRNA target prediction, and comparative genomics. The project is open source, distributed under the MIT license, and is actively maintained on GitHub. Typical users are molecular biologists and computational genomics researchers who require rapid, accurate motif scanning without the overhead of more extensive sequence‑analysis suites. The tool’s lightweight design and straightforward API make it suitable for incorporation into custom pipelines or for standalone use in teaching laboratories.