*  Table of Contents | Genetics
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms Francesca Rizzato, Alex Rodriguez, Xevi ... Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between ... Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form ... Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations Open Access ...
  http://www.genetics.org/content/207/2/
*  Point accepted mutation - Wikipedia
... th amino acid with the i {\displaystyle i} th amino acid, to the probability of these amino acids being aligned by chance. The ... the point mutation has been accepted into the genetic pool. The 20 amino acids translated by the genetic code vary greatly by ... The molecular clock hypothesis predicts that the rate of amino acid substitution in a particular protein will be approximately ... Based on the abundance of amino acids in proteins, the probability of the j {\displaystyle j} th amino acid being the original ...
  https://en.wikipedia.org/wiki/Point_accepted_mutation
*  BLOSUM - Wikipedia
... and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds ... The 20 amino acids translated by the genetic code vary greatly by the physical and chemical properties of their side chains. ... However, these amino acids can be categorised into groups with similar physicochemical properties. Substituting an amino acid ... Two major forces drive the amino-acid substitution rates away from uniformity: substitutions occur with the different ...
  https://en.wikipedia.org/wiki/BLOSUM
*  UniProtKB/SwissProt variant VAR 010578
The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid ... Although found in NIDDM patients, genetic variations of HK2 do not contribute to the disease (PubMed:7883122, PubMed:7883123). ... Lowest score: -4 (low probability of substitution).. *Highest score: 11 (high probability of substitution). ... Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss- ...
  https://web.expasy.org/variant_pages/VAR_010578.html
*  Profile for Thomas Charles Terwilliger
Zabin, H., Horvath, M. P. and T. C. Terwilliger (1991). Approaches to predicting effects of single amino acid substitutions on ... 1988). A genetic selection for temperature-sensitive variants of the bacteriophage f1 gene 5 protein. Nucl. Acids Res. 16, 9027 ... 1987). Isomorphous replacement: effects of errors on the phase probability distribution. Acta Crystallographica A43, 6-13. ... Nucleic Acids Res. 39, e125.. Lockard, M. A., Listwan, P., Pedelacq, J.D., Cabantous, S., Nguyen, H., Terwilliger, T.C., Waldo ...
  http://www.lanl.gov/expertise/profiles/view/thomas-terwilliger
*  Tenofovir vs. Tenofovir Plus Entecavir in Entecavir-Resistant Chronic Hepatitis B - Tabular View - ClinicalTrials.gov
... appears to occur through a two-hit mechanism with initial selection of M204V/I mutation followed by amino acid substitutions at ... Probability of reaching complete HBV DNA suppression was not decreased in patients with ADV or ETV-resistance. ... which has a low genetic barrier to resistance. ...
  https://clinicaltrials.gov/ct2/show/record/NCT01639092?term=hepatitis+b&recr=Open
*  UniProtKB/SwissProt variant VAR 005086
The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid ... Important genetic factors have been indicated by familial occurrence and bilateral involvement. Mutations at more than one ... Lowest score: -4 (low probability of substitution).. *Highest score: 11 (high probability of substitution). ... Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss- ...
  https://web.expasy.org/variant_pages/VAR_005086.html
*  Computational phylogenetics - Wikipedia
... substitution model that encodes a hypothesis about the relative rates of mutation at various sites along the gene or amino acid ... The use of substitution models is necessitated by the fact that the genetic distance between two sequences increases linearly ... As time since the divergence of two taxa increase, so does the probability of multiple substitutions on the same site, or back ... In molecular studies, a primary problem is in producing a multiple sequence alignment (MSA) between the genes or amino acid ...
  https://en.wikipedia.org/wiki/Computational_phylogenetics
*  Philosophical Transactions of the Royal Society B: Biological Sciences
... of nucleotide substitution or amino acid replacement allow nucleotide or amino acid types to have different probabilities, but ... For the universal genetic code, the stop codons are TAA, TAG and TGA, and this means that . ... At the protein level, the stationary probability of amino acid sequence I for this neutral model will be the sum of over all ... In order to fit our model to a profile HMM, we match equation (3.6) to the probability PHMM(I) of amino acid sequence I ...
  http://rstb.royalsocietypublishing.org/content/363/1512/3931.full
*  Gene Disease Database - Wikipedia
The data provided for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious ... The score is the normalized probability that the amino acid change is tolerated so scores near 0 are more likely to be ... A. Homosh, "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders," Nucleic Acids ... that predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physic ...
  https://en.wikipedia.org/wiki/Gene_Disease_Database
*  UniProtKB/SwissProt variant VAR 000128
The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid ... It is the most common genetic disease in Caucasians, with a prevalence of about 1 in 2'000 live births. Inheritance is ... Lowest score: -4 (low probability of substitution).. *Highest score: 11 (high probability of substitution). ... Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss- ...
  https://web.expasy.org/variant_pages/VAR_000128.html
*  Wild sparrow study traces social behaviors in the field to specific gene
Most of them involve substitutions of single amino acids-substitutions that have arisen by genetic mutations in the persons in ... An experimental test on the probability of extinction of new genetic variants. Nature Communications, September 2013 DOI: ... dependent pheromone-controlled conserved molecular mechanisms of alternative splicings of pre-mRNA and amino acid substitutions ... dependent pheromone-controlled conserved molecular mechanisms of alternative splicings of pre-mRNA and amino acid substitutions ...
  https://phys.org/news/2014-01-wild-sparrow-social-behaviors-field.html
*  UniProtKB/SwissProt variant VAR 021009
The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid ... Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational ... Lowest score: -4 (low probability of substitution).. *Highest score: 11 (high probability of substitution). ... Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss- ...
  http://web.expasy.org/variant_pages/VAR_021009.html
*  Paralogue annotation identifies novel pathogenic variants in patients with Brugada syndrome and catecholaminergic polymorphic...
In a clinical setting, the identification of a novel single amino acid substitution in a gene associated with inherited disease ... family can then be used to annotate the equivalent amino acid of other members of the family for which no clinical genetic ... probability of pathogenicity when found in clinically affected individuals.8 Here, over 80% of disease-causing variants in ... To distinguish aligned amino acids that are truly functionally equivalent from alignment artefacts, an amino acid alignment ...
  http://jmg.bmj.com/content/early/2013/10/17/jmedgenet-2013-101917.full
*  Structural Biochemistry/Bioinformatics/Sequences Alignments - Wikibooks, open books for an open world
Identical amino acid matches are also given points in a substitution matrix. There many types of substitution matrix that have ... Probability of Identity[edit]. If the 2 sequences are greater than 25% alike in a chain of at least 100 amino acids, the ... These contain numerous entries that are the DNA sequence of genes and other DNAs such as genetic mapping markers discover and ... Amino acids have a certain ability to mutate into another amino acid. Hydrophobic amino acids, (i.g. Valine) have greater ...
  https://en.wikibooks.org/wiki/Structural_Biochemistry/Bioinformatics/Sequences_Alignments
*  Enzootic transmission of yellow fever virus, Venezuela. - Free Online Library
Table 2. Nucleotide and amino acid divergence among individual YFV genes of 9 representative YFV strains compared to the ... A total of 5 substitutions delineated the Venezuelan sequences (Figure 2). Conclusions Our phylogeographic analysis supports in ... Similar results have been shown for Peru (6), Brazil, and Trinidad (4). The high posterior probabilities, ,0.99, observed at ... The 9 strains selected for comparisons represent the full spectrum of known YFV genetic diversity (Table 2; Figure 2). The most ...
  https://www.thefreelibrary.com/Enzootic+transmission+of+yellow+fever+virus%2C+Venezuela-a0398951822
*  The arc of evolutionary genetics is long
That means that they actually effect changes in amino acid and so function. This is very unlikely, so the inference must be ... beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable ... A simple explanation for what's going on above is that only a small fraction of genetic changes are beneficial, and so neutral ... Once a selectively favored mutant avoids extinction its probability of sweeping to fixation is rather high. In contrast, a ...
  http://blogs.discovermagazine.com/gnxp/2009/10/the-arc-of-evolutionary-genetics-is-long/
*  A Large Candidate Gene Survey Identifies the KCNE1 D85N Polymorphism as a Possible Modulator of Drug-Induced Torsades de...
This variant leads to an amino acid substitution from aspartic acid to asparagine at position 85 of the translated protein (Asp ... To account for genetic variation in regions surrounding each gene, we considered upstream and downstream genetic data in the ... We planned to take forward to the DARE follow-up set any SNP with a probability value of ,0.01 for both drug-drug-exposed and ... Genetic variations of kcnq1, kcnh2, scn5a, kcne1, and kcne2 in drug-induced long qt syndrome patients. J Mol Med. 2004; 82: 182 ...
  http://circgenetics.ahajournals.org/content/5/1/91.full
*  Dynamic role of the tether helix in PIP2-dependent gating of a G protein-gated potassium channel | JGP
A tyrosine substitution at 6′K increases agonist-independent basal current. (a) Structures of amino acids introduced at 6′K in ... c) Probability of hydrogen bonding between 9′E and 6′K/Y. (d) Probability of hydrogen bonding for K64, K90, 0′K, 5′K, and 6′K/Y ... Behavioral and genetic evidence for GIRK channels in the CNS: Role in physiology, pathophysiology, and drug addiction. Int. Rev ... with different amino acid substitutions at the 6′ position. Note the reduced alcohol responses for 6′Y (n = 8-18). Bars ...
  http://jgp.rupress.org/content/149/8/799
*  UniProtKB/SwissProt variant VAR 018629
The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid ... Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk ... Lowest score: -4 (low probability of substitution).. *Highest score: 11 (high probability of substitution). ... Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss- ...
  http://web.expasy.org/variant_pages/VAR_018629.html
*  Genealogical Evidence for Positive Selection in the nef Gene of HIV-1 | Genetics
Bars represent the probability of substitutions under positive selection (with ≥90% posterior probability) and the amino acid ... Although this was taken to mean that all amino acid changes are neutral and therefore fixed by genetic drift alone, in reality ... and two amino acid substitutions were reconstructed on the branch leading to the 41-mo time point and again both amino acid ... Reconstructing allele substitutions in the nef gene: A parsimony method was next used to reconstruct the unambiguous amino acid ...
  http://www.genetics.org/content/153/3/1077
*  Benchmarking Multi-Rate Codon Models
... amino acid substitution biases are incorporated into codon models by weighted partitioning of empirically-derived amino acid ... Because the genetic code itself is not transitive, i.e. one can easily find triplets of amino-acid residues (for instance ), ... and assign substitutions to rate classes randomly with uniform probability, i.e. on average the same number of rates are ... of synonymous substitution rates for all possible one-nucleotide substitutions that don't change the amino acid, and is its non ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2908124/?lang=en-ca
*  Ka/Ks ratio - Wikipedia
Some amino acids are chemically similar to one another, whereas other substitutions may place an amino acid with wildly ... The genetic code is written in DNA sequences as codons, groups of three nucleotides. Each codon represents a single amino acid ... it is impossible to exactly determine the number of multiple substitutions. The maximum-likelihood approach uses probability ... For example, the DNA codons TTT and TTC both code for the amino acid Phenylalanine, so a change from the third T to C makes no ...
  https://en.wikipedia.org/wiki/Ka/Ks_ratio
*  Sandwalk: Is it impossible to educate Intelligent Design Creationists on evolutionary theory?
... the probability of each required substitution would be low, and the probability of all in combination would be virtually zero ... Amongst proteins primary amino acid sequences are inordinately more diverse than are functionally relevant secondary and ... They call it DNA -- short for the almost unpronounceable word, deoxyribonucleic acid. DNA is a genetic code, like a master ... the probability of each required substitution would be low, and the probability of all in combination would be virtually zero ...
  http://sandwalk.blogspot.com/2015/03/is-it-impossible-to-educate-intelligent.html
*  Genetics - Medical Microbiology - NCBI Bookshelf
Genetic material must replicate accurately so that progeny inherit all of the specific genetic determinants (the genotype) of ... Bacterial viruses (bacteriophages or phages) have DNA or RNA as genetic material. The two essential functions of genetic ... Expression of specific genetic material under a particular set of growth conditions determines the observable characteristics ( ... The genetic material of bacteria and plasmids is DNA. ... Other substitutions cause one amino acid to be replaced by ...
  https://www.ncbi.nlm.nih.gov/books/NBK7908/?report=reader