PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes

• Published in: Bioinformatics Vol. 20; no. 5; pp. 629 - 635
• Main Authors: Lavigne, R., Sun, W.D., Volckaert, G.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 22.03.2004; Oxford Publishing Limited (England)
• Subjects: Bacteria; Bacteriophages - genetics; Base Sequence; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Regulation, Viral - genetics; General aspects; Genes, Regulator - genetics; Genome, Viral; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Software; Nucleotide sequence; Podoviridae; Genomics; Prediction; Knowledge; IS element; Virus; Gene; Phage T7; Genome; Learning algorithm; Phage T3; Phage
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btg456

Motivation: In silico genome analysis of bacteriophage genomes focuses mainly on gene discovery and functional assignment. The search for regulatory elements contained within these genome sequences is often based on prior knowledge of other genomic elements or on learning algorithms of experimentally determined data, potentially leading to a biased prediction output. The PHage In silico Regulatory Elements (PHIRE) program is a standalone program in Visual Basic. It performs an algorithmic string-based search on bacteriophage genome sequences to uncover and extract subsequence alignments hinting at regulatory elements contained within these genomes, in a deterministic manner without any prior experimental or predictive knowledge. Results: The PHIRE program was tested on known phage genomes with experimentally verified regulatory elements. PHIRE was able to extract phage regulatory sequences correctly for bacteriophages T7, T3, ϕYeO3-12 and λ, based solely on the genome sequence. For 11 bacteriophages, new predictions of conserved phage-specific putative regulatory elements were made, further corroborating this approach. Availability: http://www.agr.kuleuven.ac.be/logt/PHIRE.htm. Freely available for academic use. Commercial users should contact the corresponding author.