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*  Gap penalty
However, not all indels are frameshift mutations. If indels occur in trinucleotides, the result is an extension of the protein ... Garcia-Diaz, Miguel (2006). "Mechanism of a genetic glissando: structural biology of indel mutations". Trends in Biochemical ... These two replication errors are insertions and deletions of single DNA bases from the DNA strand (indels). Indels can have ... or a frameshift mutation that may render the protein inactive. The biological consequences of indels are often deleterious and ...
*  CRISPR
By contrast, since Cas9 cuts only 3 bp upstream of the PAM site, the NHEJ pathway results in indel mutations which destroy the ... Kidney organoids with mutations in a gene linked to FSGS developed junctional defects between podocytes, the filtering cells ... Mutation studies confirmed this hypothesis, showing that removal of cas1 or cas2 stopped spacer acquisition, without affecting ... Phages can continue to infect their hosts given point mutations in the spacer. Similar stringency is required in PAM or the ...
*  Von Hippel-Lindau disease
The remaining 60-70% of VHL disease is caused by the truncation of pVHL by nonsense mutations, indel mutations or splice site ... 30-40% of mutations in the VHL gene consist of 50-250kb deletion mutations that remove either part of the gene or the whole ... There are over 1500 germline mutations and somatic mutations found in VHL disease. Every cell in the body has 2 copies of every ... A new novel missense mutation in VHL genes c.194 C>T, c.239 G>A, c.278 G>A, c.319 C>G, c.337 C>G leading to the following ...
*  Duplex sequencing
"Detecting ultralow-frequency mutations by Duplex Sequencing". Nature Protoc., vol. 9 no. 11, 2586-606. 2014. PMID 25299156. T. ... indels and copy number variations. Duplex sequencing and the significant increase of sequencing accuracy has important impacts ... A. Y. Maslov, W. Quispe-Tintaya, T. Gorbacheva, R. R. White, and J. Vijg, "High-throughput sequencing in mutation detection: A ... Duplex sequencing theoretically can detect mutations with frequencies as low as 5 x 10−8 that is more than 10,000 fold higher ...
*  Indel
Indels can be contrasted with a point mutation. An indel inserts and deletes nucleotides from a sequence, while a point ... In coding regions of the genome, unless the length of an indel is a multiple of 3, it will produce a frameshift mutation. For ... Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM ... It has been shown that genomic regions with multiple indels can also be used for species-identification procedures. An indel ...
*  List of RNA-Seq bioinformatics tools
... and detect candidate mutations, indels, splice or fusion junctions in each single read. Importantly, CRAC improves its ... It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms. The ... Novoalign tolerates up to 8 mismatches per read, and up to 7bp of indels. It is able to deal with bisulphite data. Output in ... Highly tolerant of substitution errors and indels, and very fast. Supports output of all SAM tags needed by Cufflinks. No limit ...
*  Nucleic acid sequence
... mismatches can be interpreted as point mutations and gaps as insertion or deletion mutations (indels) introduced in one or both ... Nguyen, T; Brunson, D; Crespi, C L; Penman, B W; Wishnok, J S; Tannenbaum, S R (April 1992). "DNA damage and mutation in human ... the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon and other mutations ... assumes that the effects of mutation and selection are constant across sequence lineages. Therefore, it does not account for ...
*  Multiple sequence alignment
Point mutations and insertion or deletion events (called indels) can be detected. Multiple sequence alignments can also be used ... Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino ... and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. ... Similarly, the evolutionary operator of point mutations can be used to define an edit distance for coding sequences, but this ...
*  Pseudogene
Various mutations (such as indels and nonsense mutations) can prevent a gene from being normally transcribed or translated, and ... Mutations that disrupt either the structure or the function of either of the two genes are not deleterious and will not be ... The current work may also help to explain why we are able to live with 20 to 100 putative homozygous loss of function mutations ... Another more recent example of a disabled gene links the deactivation of the caspase 12 gene (through a nonsense mutation) to ...
*  Frameshift mutation
A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels (insertions ... There are at least two other types of recognized point mutations, specifically missense mutation and nonsense mutation. A ... Both of these mutations commonly occur in tandem with at least one other mutation. They both lead to a small decrease in the ... Mutations in the β-hexosaminidase A (Hex A) gene are known to affect the onset of Tay-Sachs, with 78 mutations of different ...
*  Isozyme
... indel) events that affect the DNA coding sequence of the gene. As with any other new mutations, there are three things that may ... then the mutation may be selectively neutral and subject to genetic drift.[citation needed] In rare cases, the mutation may ... However, if the mutations do not immediately prevent the enzyme from functioning, but instead modify either its function, or ... in which case the mutation may cause an increase in fitness, and be favoured by natural selection.[citation needed] An example ...
*  Surveyor nuclease assay
... usually small indels), which will be difficult to identify using Sanger sequencing. Point mutations and indels can be detected ... It also detects Indels up to at least 12 bp. Surveyor nuclease assay can also detect multiple mutations in the same fragment. ... Multiple mutations can be detected by the presence of several fragments. One of the main advantages of detecting mutations and ... Therefore, this must be followed with additional techniques in order to pinpoint the mutation or map multiple mutations in the ...
*  Adaptive evolution in the human genome
... indels), rather than point mutations (Lunter et al. 2006), although the method has only been applied to examine patterns of ... Alternatively, the adaptive mutations may be the ones which reduce the chance of disease arising due to other mutations. ... This includes the concept of "surfing mutations", where new mutations can be propagated with a population expansion (Klopfstein ... of new advantageous mutations in the human genome, but this DFE is difficult to infer because new advantageous mutations are ...
*  Insertion (genetics)
Indel Insertional mutagenesis Loss-of-Function Mutations Gain-of-Function Mutations Banavali, Nilesh K. "Partial base flipping ... Frameshift mutations will alter all the amino acids encoded by the gene following the mutation. Usually, insertions and the ... Trinucleotide repeats are classified as insertion mutations and sometimes as a separate class of mutations. Insertions can be ... A frameshift mutation, an alteration in the normal reading frame of a gene, results if the number of inserted nucleotides is ...
*  Sequence alignment
... mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in ... Gap penalties account for the introduction of a gap - on the evolutionary model, an insertion or deletion mutation - in both ... A series of matrices called PAM matrices (Point Accepted Mutation matrices, originally defined by Margaret Dayhoff and ... the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon and other mutations ...
*  CAPP-Seq
Another advantage is that CAPP-Seq can not only detect point mutations but it can also detect indels, structural variations, ... RI represents a patient level recurrence frequency estimated for somatic mutations and all mutations. Known and driver ... RI is the number of mutations per kilobase of a given genomic locus of a patient carrying particular mutations. ... For the indel calls, statistical significance is calculated applying a separate method that used a strand specific analysis by ...
*  Genetic code
... whereas nonsense mutations result in a stop codon. Mutations that disrupt the reading frame sequence by indels (insertions or ... Missense mutations and nonsense mutations are examples of point mutations that can cause genetic diseases such as sickle-cell ... Although most mutations that change protein sequences are harmful or neutral, some mutations have benefits. These mutations may ... These mutations usually result in a completely different translation from the original, and likely cause a stop codon to be ...
*  Margaret Oakley Dayhoff
From this mutation matrix, a Dayhoff scoring matrix may be constructed. Along with a model of indel events, alignments ... Percent Accepted Mutation), MDM (Mutation Data Matrix), or Dayhoff. They are derived from global alignments of closely related ... "How to Compute Mutation and Dayhoff Matrices". www.biorecipes.com. Retrieved October 22, 2016. "MARGARET OAKLEY DAYHOFF, 57; ... She originated one of the first substitution matrices, point accepted mutations (PAM). The one-letter code used for amino acids ...
*  1000 Genomes Project
Gaucher disease (mutations in the GBA gene), Crohn's disease (mutation of NOD2) and familial hypertrophic cardiomyopathy ( ... demonstrated that indels account for 90.4% of all observed variations in the sequence of the major histocompatibility locus ( ... mutations in MYH7, TNNT2, TPM1 and MYBPC3) are all examples of negative selection. These disease mutations are primarily ... Besides mutations, SNPs and other structural variants such as copy-number variants (CNVs) are contributing to the genetic ...
*  MutationTaster
Mutation Taster is written in Perl and can process Next-generation sequencing data of all major platforms (Roche 454, Illumina ... such as indels) Multiple tests are performed to determine the nature of the given SNP. These tests comprise (among others): ... Many genetic disorders can be caused by mutation of a single gene. New sequencing techniques however, have shown that a single ... The challenge of prediction tools is thus to filter harmless mutations from disease-causing ones. It is important to note that ...
*  DNA mismatch repair
... causing mutations that bear a signature of POLH activity. Recognizing and repairing mismatches and indels is important for ... In addition to a very high mutation burden, MMR deficiencies result in an unusual distribution of somatic mutations across the ... Supek, Fran; Lehner, Ben (2017-07-27). "Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to ... Sporadic cancers with a DNA repair deficiency only rarely have a mutation in a DNA repair gene, but they instead tend to have ...
*  Human evolutionary genetics
Many different mutations can inactivate a gene, but few will change its function in a specific way. Inactivation mutations will ... DNA sequences may however also differ by insertions and deletions (indels) of bases. These are usually stripped from the ... The mutation rate is higher in the male germ line, therefore the divergence in the Y chromosome-which is inherited solely from ... Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny ...
*  Sequenom
... Oncomap Version 3 - "core" set interrogates ~450 mutations in 35 genes. An "extended" set interrogates ~700 mutations ... INDELS) and copy number variation (CNV) assays for use in the investigation of variants with demonstrated relevance to drug ... In total, 417 mutations are identified. MassARRAY spectrometry is more sensitive than PreTect HPV-Proofer and Consensus PCR for ... Sequenom OncoCarta(OncoMap) identifies 396 unique "druggable" or "actionable" mutations in 33 cancer genes. ...
*  Genetic variation
Random mutations are the ultimate source of genetic variation. Mutations are likely to be rare and most mutations are neutral ... Small-scale sequence variation (< 1Kbp) includes base-pair substitution and indels. Large-scale Structural variation (>1Kbp) ... Polyploidy is an example of chromosomal mutation. Polyploidy is a condition wherein organisms have three or more sets of ... Genetic variation is brought about, fundamentally, by mutation, which is a permanent change in the chemical structure of ...
*  Gene polymorphism
An example of this phenomenon is the mutation of somatic cells leading to cancer in a specific area of an organism's body. Gene ... Nowadays, two million INDELs have been discovered in approximately seventy-nine various humans genomes. Furthermore, small ... Once amplified, a number of methods can be used to identify a mutation or polymorphism in the coding sequence including DNA ... Gene polymorphisms generally occur in populations at a frequency of 1% or more while mutations usually occur at a frequency of ...