Even a recent "alignment-free" study using so-called feature frequency profiles [11] placed the Shigella species into the E. coli strains.
In recent years, alignment methods that compare two profiles, the statistical models that represent protein families, have been shown to improve alignment quality and homolog recognition over sequence sequence methods such as BLAST (Altschul et al., 1997) and sequence profile methods such as PSI-BLAST (Altschul et al., 1997; Schaffer et al., 2001).
We use the recent latitudinal alignment of Ulysses and Voyager 2 to determine the solar wind slowdown due to interstellar neutrals at 80 AU and estimate the interstellar neutral density.
In recent years, manifold alignment methods have aroused a great of interest in the machine learning community which construct a common latent space shared by multiple input data sets.
For improving the search accuracy, we used our recent (large scale) alignment of σ70 promoter elements in E. Coli [ 19].
BEAMS [ 14] is another recent multiple network alignment algorithm, which first extracts the so-called "backbones", or the minimal set of disjoint cliques in the filtered similarity graph, and then iteratively merges these backbones to maximize the overall alignment score.
We tested DOMAIN to identify conserved protein complexes in the yeast fly and yeast worm protein interaction networks, and the experimental results show that DOMAIN exhibits better performance than two recent pairwise network alignment methods in most performance metrics.
In a recent study, the alignment at distance was recorded with a mean of 10.9 years after first surgery, forty-five percent of patients being within 8Δ of orthotropia [ 29].
NetDis: This most recent graphlet-based alignment-free network comparison method (Ali et al., 2014 ) first obtains ego-networks of radius two (i.e. subgraphs induced on the nodes that are in the first and second neighbourhood of a given node) for each node in a given network and computes the number of graphlets in each of the resulting ego-networks.
Recent progress in sequence alignment and structure prediction has suggested the importance of variable gap penalties in protein sequence alignment [51].
