genWave
Genomic Island Finder
genWave uses the daubechies wavelet transform on a GC signal to identify genomic regions that may represent a horizontal transfer (e.g. pathogenicity island). The code for this version has not been optimized, so analyses may take a couple minutes depending on the size of the genome submitted. Please enter an input file of either raw DNA sequence or a FASTA format DNA sequence file.
DNA Sequence File:
To see an example of this tool on N. meningitidis B, do not select a file above and hit submit.



Advanced Options:
The following default values will work in most cases.
Vanishing Moments:
Window Size:
Scalogram Cut-off:


vanishing_moments The number of desired vanishing moments the daubechies filter is to contain. It must be an even number between 1 and 10 (inclusive).
scalogram_cutoff This is a number between 1 and log_base2(length(sequence)/window_size) (inclusive) representing the low frequency cut-off used to select the wavelet coefficients for the inverse wavelet transform. I would recommend trying 7 first, then inspect the scalogram graph produced to see if it accurately captures the low frequency peak. This peak may not be very distinct. The smaller it is, the less likely there are any low frequency events. I would also look at the output signal to see if there's much noise. To reduce the noise, decrement this value and try again, or pick a value from the scalogram that best defines the end of the low frequency peak. Note the you will lose resolution the smaller you make the cutoff.
window_size This is the size of the "basepair window". It's otherwise known as a "smooting factor". Optimal values are between 4 and 10 (inclusive).

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