Related papers: From Best Hits to Best Matches
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context--as short as single maximal matches--also provides an effective means to…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
It is common to use reciprocal best hits, also known as a boomerang criterion, for determining orthology between sequences. The best hits may be found by blast, or by other more recently developed algorithms. Previous work seems to have…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Considering the high heterogeneity of the ontologies pub-lished on the web, ontology matching is a crucial issue whose aim is to establish links between an entity of a source ontology and one or several entities from a target ontology.…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Typically an ontology matching technique is a combination of much different type of matchers operating at various abstraction levels such as structure, semantic, syntax, instance etc. An ontology matching technique which employs matchers at…