Detect DNA words
choose a species: The analysis will be carried out with either the choosen genome assemly from our DB
upload a sequence: or with the uploaded sequence
The DNA word(s): The words need to be separated by : like CGG:CGC:CGA
The strand if both strands is chosen, the program analyses also the reverse complementary DNA words. The selection has no influence if genomic entities are analysed!
Distance parameters
Chromosome intersection: For each chromosome the first intersection between the observed and the theoretical distance distribution is detected. This distance is then taken as the maximal distance between two DNA words or entities
Genome intersection: Warning: This is very slow!
In a first round, the observed distance distribution for the whole genome is detected. Then, the intersection with the theoretical distribution is calculated. The resulting distance is used as parameter (max. distance) for all chromosomes.
Percentile: The percentlile (between 1 and 100) of the observed distance distribution which should be used as distance parameter (for each chromosome a different max. distance will be used). For example. percentile = 50 would be the median
Fixed distance: The max. distance for each chromosome
P-value: The p-value filter. Just clusters with lower p-values will be present in the output