Also, each node in a splicing graph is evaluated instead of each exon, with each read that contains a k-mer within a node contributing to that node.
Therefore in the de Bruijn graph, sp-branches started from a common k-mer in similar subspecies usually have (converge to) another common k-mer within a short distance, while cr-branches started from a common k-mer in multiple species seldom have another common k-mer within a short distance.
Briefly, the probability of observing any specific k-mer within a motif is the sum of the probabilities of observing the motif at all positions within the motif, including those that span the boundaries between the motif and the background.
By removing those branches that cannot converge to another k-mer within a short distance, the genome of a species with several subspecies can be represented by connected components in the de Bruijn graph, where each component represents similar contigs in the genomes from similar subspecies.
Candidate k-mers are stored in a data structure such as a Hamming graph, which connects k-mers within a fixed distance, or a Bloom filter.
In Hammer, we proposed the simple choice of the consensus string as a way to correct the k-mers within a cluster.
It is possible, however, to develop a more sophisticated approach that allows the identification of multiple correct k-mers within a cluster (Wijaya et al., 2009).
Any repetitive k-mers within a string are counted only once since only the unique counts are used to create the quotient.
Recent approaches have taken steps in the right direction by looking together at all k-mers within a small Hamming neighborhood.
Stanley et al. analyzed the distribution of 1- to 4-mers within a wide variety of organisms and found that some tend to cluster within genomes (usually in non-coding regions) and others tend to "repel" each other [ 12, 13].
There is no dedicated solution in T-IDBA that solves the issue of erroneous k-mers within a component and methods for isolating components are not sensitive to low-expressed isoforms.
