In practice, DTW first evaluates the local alignment distance between each pair of elements in order to obtain a distance matrix.
The correlation analysis of alignment distance vs. EDE distance shows a clear correlation.
The efficiency of random shearing was tested by plotting mapping frequency against the alignment distance from the 3′ end of cDNA.
The Sankoff algorithm tries to minimize the sum of alignment distance and free energy of the involved RNA molecules.
This procedure allows us to compare our approach to MOTHUR and DOTUR, both of which use the alignment distance cutoff and ESPRIT, which uses the k-mer distance cutoff.
Phylogenetic networks can be computed from a wide range of data, including multiple sequence alignments, distance matrices, set of trees, clusters, splits, rooted triplets, or unrooted quartets.
Using the first (best) alignment retumed, the distance of the 5' end of the target sequence from the 3' end of the mRNA or EST in the nr database was calculated.
Of the 20 chromosomes (1 18, X and Y), 4,529 of 5,398 (83.9%) pairwise alignments were intrachromosomal and most pairwise alignments were within the distance of 1 Mb between each other.
The intuition underlying Equation (8) is that if the alignment is good, the distance of a sequence residue pair shall match well with that of their aligned template residue pair.
Therefore, poor homology along oligo 3' region against interrogating transcripts can be expected to be less influential on hybridization intensity, as confirmed in our data No effect could be detected when selection was made for distance of alignment from 3' side (data not shown).
In particular, the mean distance of alignments to the pseudoautosomal regions was not closer than 95% (n = 1000 replications) of simulated randomized alignment positions.
