Coding redundancy

This still makes perfectly good sense, perhaps better sense than the first version, but it is certainly giving us a different message. The DNA equivalent is a point mutation swapping one base for another and the likely consequence is a swap of one amino acid for another. (Because of coding redundancy there is also the possibility of a silent point mutation and we shall come back to that shortly.)... 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

It should be pointed out that it is probably not necessary to make as many redundant taps as called for in a code test. However, as long as taps... 

Many modem computer codes (e.g. GAUSSIAN98) employ so-called redundant internal coordinates] this means that we use all possible internal coordinates, of which there will generally be more than 3N — 6. Only a maximum of 3M — 6 will be linearly independent, and we essentially throw away the remainder at the end of the full calculation. Here is ethene, done using redundant internal coordinates. 

Thus the coding has reduced the entropy of the source somewhat, since it is unable to supply unique code words for all sequences on the other hand, the redundancy per source letter in the code words, Nb — S(W)IN, can be made arbitrarily small. 

D A. Huffman, "A Method for the Construction of Minimum Redundancy Codes, Proc. Sept. 1952. <... 

In order to obtain the preferred term for a given drug, you have to pull drug record numbers, where sequence number 1 is 01 and sequence number 2 is 001. Also, redundancies in the resulting data set must be stripped out with first-dot processing or a NODUPKEY on a PROC SORT. The following SAS code shows how to get preferred terms from WHODrug. 

In Section 1.5 we briefly discussed the relationships of equality and inequality constraints in the context of independent and dependent variables. Normally in design and control calculations, it is important to eliminate redundant information and equations before any calculations are performed. Modem multivariable optimization software, however, does not require that the user clearly identify independent, dependent, or superfluous variables, or active or redundant constraints. If the number of independent equations is larger than the number of decision variables, the software informs you that no solution exists because the problem is overspecified. Current codes have incorporated diagnostic tools that permit the user to include all possible variables and constraints in the original problem formulation so that you do not necessarily have to eliminate constraints and variables prior to using the software. Keep in mind, however, that the smaller the dimensionality of the problem introduced into the software, the less time it takes to solve the problem. 

Currently, a good LP solver running on a fast (> 500 mHz) PC with substantial memory, solves a small LP in less than a second, a medium-size LP in minutes to tens of minutes, and a large LP in an hour or so. These codes hardly ever fail, even if the LP is badly formulated or scaled. They include preprocessing procedures that detect and remove redundant constraints, fixed variables, variables that must be at bounds in any optimal solution, and so on. Preprocessors produce an equivalent LP, usually of reduced size. A postprocessor then determines values of any removed variables and Lagrange multipliers for removed constraints. Automatic scaling of variables and constraints is also an option. Armed with such tools, an analyst can solve virtually any LP that can be formulated. 

This approach can be quite damaging. Each implementor provides identified defensive checks in the code, but none of the interfaces documents what is guaranteed to be checked and by whom or what outcome is guaranteed in the event of those errors. Responsibilities become blurred, and the code becomes littered with disorganized, redundant, and inadequate checking and handling of exception cases. 

The simplest way of doing this is to import the models into a single package, and then define invariants defining how the attributes from one view are related to those from another, just as you would for redundant attributes. However, you may then need a separate refinement stage to get to the code. 

A base substitution can also result in the formation of a new inappropriate terminator (or non-sense) codon, and are thus known as non-sense mutations. The polypeptide formed from such mutated genes will be shorter than normal and is most likely to be inactive. Owing to the redundancy of the genetic code, about a quarter of all possible base substitutions will not result in an amino acid replacement and will be silent mutations. 

When parameterizing the Jacobian, obviously, redundancies should be avoided. In particular, if a metabolite affects a reaction as a substrate, as well as an allosteric effector, the interaction should be coded into one parameter, rather than a sum of two parameters. Unfortunately, to detect and avoid higher order redundancies is no easy task and we are not aware of any straightforward solution. 

Genetic code Start AUG (also codes for Met) Stop UAG,UGA,UAA Unambiguous (1 codon = 1 amino acid) Redundant (1 amino acid >1 codon) often differ at base 3 ... 

In order to eliminate parameters that are correlated to each other, we calculate their Pearson correlation coefficients (25). Linearly uncorrelated parameters have Pearson correlation coefficients close to zero and likely describe different aspects of the phenotype under study (exception for non-linearly correlated parameters which cannot be scored using Pearson s coefficient). We have developed an R template in KNIME to calculate Pearson correlation coefficients between parameters. Redundant parameters that yield Pearson correlation coefficients above 0.4 are eliminated. It is important to visually inspect the structure of the data using scatter matrices. A Scatter Plot and a Scatter Matrix node from KNIME exist that allow color-coding the controls for ease of viewing. 

The sequence of bases in the polynucleotide chain is also important because it determines the exact sequence of amino acids used in the synthesis of a protein. Twenty amino acids are commonly found in proteins, while only four bases are used in the DNA molecule. Thus, more than one base must specify each amino acid. The genetic code is in fact read as triplets and there are 64 possible triplet combinations using 4 nucleotides. Each triplet of nucleotides is termed a codon, and given the redundancy, some amino acids are specified by more than one codon. 

The existence of 64 - 20 = 44 excess codons allows a valuable redundancy in the genetic code. It also permits the signaling for the start and end of the protein chain. 

The most common changes in mitochondria (and the only code changes that have been observed in cellular genomes) involve termination codons. These changes affect termination in the products of only a subset of genes, and sometimes the effects are minor because the genes have multiple (redundant) termination codons. 

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