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Motif finding
Motif finding

Preliminary review / Publisher`s description: This self
Preliminary review / Publisher`s description: This self

... mathematicians to optimization and related topics that have been ignored up to now in the occidental academic world. 2. The book is totally self-contained, although some familiarity with basic calculus and algebra could help the reader. The first contact with each topic is intuitive, showing the geo ...
Tracking the algal origin of the Ulva bloom in the Yellow Sea by a
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... unambiguous. But the ITS nrDNA alignment contained many insertions and deletions. The combined data set contained the ITS nrDNA and rbcL sequences (Hayden et al., 2003). Prior to analysis of the combined data, the incongruence length difference test was conducted. The phylogenetic trees were constru ...
Constant-Time LCA Retrieval
Constant-Time LCA Retrieval

... If u is an ancestor of v then all those nodes visited between u and v are in u’s subtree, and thus the depth-number assigned to u is minimal in I. If u is not an ancestor of v, then all those nodes visited between u and v are in lca(u,v)’s subtree, and the traversal must visit lca(u,v). Thus the min ...
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Monte-Carlo Tree Search for the Physical Travelling Salesman
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Lecture4 - Department of Computer Science
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... • Two proteins that are almost identical, except the second protein has a 20 residue insertion into the middle of the sequence. • If the window size is 15, then the SmithWaterman alignment phase of FASTA will align the protein to either the sequence prior to or following the insertion, thus missing ...
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Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.Producing a phylogenetic tree requires a measure of homology among the characteristics shared by the taxa being compared. In morphological studies, this requires explicit decisions about which physical characteristics to measure and how to use them to encode distinct states corresponding to the input taxa. In molecular studies, a primary problem is in producing a multiple sequence alignment (MSA) between the genes or amino acid sequences of interest. Progressive sequence alignment methods produce a phylogenetic tree by necessity because they incorporate new sequences into the calculated alignment in order of genetic distance.
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