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Each method allows for a bootstrap phylogeny test with any number of replications. Neighbor joining and minimum evolution allows for an interior-branch test instead. Substitution model and parameters are the same as the distance estimation methods.
The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17 ...
This method is able to detect as low as 25 μg/ml and up to 2000 μg/ml of protein in a 65 ul sample, using standard protocol. This method may be preferred for samples containing detergents or other reducing agents. This method has a fast detection speed and low protein-to-protein variability in comparison to the BCA or Coomassie (Bradford ...
Methods (implemented by each program) that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences , gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.
Protein methods are the techniques used to study proteins. There are experimental methods for studying proteins (e.g., for detecting proteins, for isolating and purifying proteins, and for characterizing the structure and function of proteins, [1] often requiring that the protein first be purified). Computational methods typically use computer ...
BCA protein assay in a 96 well plate. The bicinchoninic acid assay (BCA assay), also known as the Smith assay, after its inventor, Paul K. Smith at the Pierce Chemical Company, [1] now part of Thermo Fisher Scientific, is a biochemical assay for determining the total concentration of protein in a solution (0.5 μg/mL to 1.5 mg/mL), similar to Lowry protein assay, Bradford protein assay or ...
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Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures.