PHIRE(PHage In silico Regulatory Elements)
Lavigne, R., Sun, W.D. and Volckaert, G. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics (2004) 20: 629-635.
Created at Katholieke Universiteit Leuven, LoGTDownload ver 1.00
The PHIRE program, a standalone program in Visual Basic, performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge.
The technique of systematically scanning the bacteriophage genome implemented in PHIRE, offers an objective way search for unusual sequence patterns in the sequence. Interpretation of these patterns can lead to functional prediction for these sequence regions. Because this is done in parallel with ORF prediction, potential genes and potential regulatory elements can be placed next to each other for functional assignment.
PHIRE systematically compares all the DNA substrings of a specified length (L) to one another, allowing a limited number of mismatches (degeneracy D) to sort out and extract the largest sets (DominantNum) of substrings that represent a unique consensus. In this manner, the entire genome is analysed on both the Watson and crick DNA strand. In order to visualize the sequences around the consensus sequence, the window size (W) can be adapted to include the sequences left and right of each selected DNA individual string.
PHIRE ver. 1.00 was implemented on a Windows 98 platform, using Visual Basic 6.0 Enterprise edition. The program requires a Windows platform (95 and above) and is optimised for systems with Pentium Pro microprocessor (Pentium II and above). This program does not require large amounts of memory, however, the running time of a genome sequence of a specific length will depend mainly on the CPU speed.