On an second experiment, we also have measured the update time and the disruption caused by our reconfiguration approach varying the number of CNs and rate (i.e., frequency) of tuple production, as well as the overhead in terms of throughput imposed by our approach.
In the SvH and GY models, the rates are proportional to the frequency of the resulting tuple (doublet or codon respectively).
The basic idea of alignment-free methods is to use the occurrence or frequency of k-tuples (k-mers, k-grams) as sequence signatures of the studied genomes or metagenomes, and use such signatures as features for the clustering or classification.
One such system is the Protégé plug-in TerMine (Frantzi et al., 2000), which suggests terms by analyzing the frequencies of word tuples in a text for a given query.
Frequencies of 2-tuples in genomes enabled the creation of a biologically plausible phylogenetic tree for mitochondrial genomes.
Genome sequence signatures refer to the frequencies of k-tuples (k-mers, k-grams) in a genome.
One is a detailed list of the positions at which each k-tuple is localized in the genomic sequence and a global table with the frequency of occurrences of each tuple in the genomic sequences (global frequency table).
This was carried out by studying the genomic frequencies of small tuples of nucleotides known as oligonucleotides.
Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences.
Third, we used the typical k-tuple distance (dk), which is based on the frequency of occurrence of the tuples in the genomic sequences and considers the length of these. 2 The dLog, given two genomes, A and B, was calculated in two steps.
