PHIRE 1.0 Description:

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.

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.

This way, the entire genome will be analysed on the Watson and crick DNA strand as well. 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 1.0 Features:

INPUT
· The input sequence can be entered in FASTa format or as a raw sequence
· PHIRE automaticaly counts the basepairs; degeneracies will be omitted from the sequence!

PARAMETERS
· (S)tring Length (L): Length of the subsequence the PHIRE algorithm will scan for. (default 20-mer sequences)
· (D)egeneracy: Number of mismatches allowed between 2 strings (default 4)
· DominantNum: Number of MaxSets PHIRE will show after analysis. The MaxSet contains the sequences and coordinates for a set of conserved subsequences
· (W)indow size: allows the display of flanking regions (left and right) of the output after analysis
· Maxset: menu which allows the display of the other sets of sequences

OUTPUT
· The output box shows the selected MaxSet
· The Finished value equals the number of substring comparisons N= G-L+1 (G= genome length; L= String Length)
· Run Time (in minutes): Time the PHIRE analysis has been running
· Time Left (in minutes): Estimated time left for the analysis
· START: start the analysis
· SAVEFILE: saves the entire output (MaxSets) in a text format.

PHIRE security information

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