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A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
It is these sequences that are the so-called 'ancestors' – the process of synthesizing the corresponding DNA, transforming it into a cell and producing a protein is the so-called 'reconstruction'. Ancestral sequences are typically calculated by maximum likelihood, however Bayesian methods are also implemented. Because the ancestors are ...
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There are many computational tools for protein structure reconstruction [1] that are usually focused on specific reconstruction tasks which include: backbone reconstruction from alpha carbons, side-chains reconstruction from backbone chain atoms, hydrogen atoms reconstruction from heavy atoms positions and recovery of protein structure from ...
Vector field reconstruction [1] is a method of creating a vector field from experimental or computer-generated data, usually with the goal of finding a differential equation model of the system. Definition
The concept of ancestral reconstruction is often credited to Emile Zuckerkandl and Linus Pauling.Motivated by the development of techniques for determining the primary (amino acid) sequence of proteins by Frederick Sanger in 1955, [9] Zuckerkandl and Pauling postulated [10] that such sequences could be used to infer not only the phylogeny relating the observed protein sequences, but also the ...
Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), [citation needed] usually an inputed sequence that is not represented in the input.