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*  Conserved non-coding sequence
Pseudogenes are vestiges of once-functional genes disabled by sequence deletions, insertions, or mutations. The primary ... A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are ... the distinction between regions with a high degree of sequence conservation and those with perfect sequence conservation is not ... since closer relatives have sequence conservation among nonfunctional elements as well. Orthologues with high sequence ...
*  Smith-Waterman algorithm
... aligns two sequences by matches/mismatches (also known as substitutions), insertions, and deletions. ... The size of the matrix is the length of one sequence plus 1 by the length of the other sequence plus 1. The additional first ... Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences ... Bioinformatics Sequence alignment Sequence mining Needleman-Wunsch algorithm Levenshtein distance BLAST FASTA Smith, Temple F ...
*  Needleman-Wunsch algorithm
Sankoff D (1972). "Matching sequences under deletion/insertion constraints". Proceedings of the National Academy of Sciences of ... NW-align: A protein sequence-to-sequence alignment program by Needleman-Wunsch algorithm (online server and source code) ... A clear explanation of NW and its applications to sequence alignment Sequence Alignment Techniques at Technology Blog ... Biologically, a large gap is more likely to occur as one large deletion as opposed to multiple single deletions. Hence we ...
*  David Sankoff
Sankoff, D. (1972). "Matching sequences under deletion-insertion constraints". Proceedings of the National Academy of Sciences ... In particular, he had a key role in introducing dynamic programming for sequence alignment and other problems in computational ... In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ... In 1971, Sankoff became interested in molecular sequence comparison and devised the first quadratic-time variant of the ...
*  Germline mutation
This long stasis period has been shown to result in a higher number of chromosomal and large sequence deletions, duplications, ... then the sequence will undergo non-homologous end joining (NHEJ). NHEJ often results in insertions or deletions within the gene ... which can then be used to mutate or repair the DNA sequence. It functions by using a specific repeated sequence of an amino ... The most common mutation seen in this disease is ΔF508, which means a deletion of the amino acid at the 508 position. If both ...
*  METAP2
Chang YH, Teichert U, Smith JA (April 1992). "Molecular cloning, sequencing, deletion, and overexpression of a methionine ... sequenced to date, suggesting their presence is important to catalytic activity. Based upon X-ray crystallographic data, ... MetAP2 is 22 percent homologous with the sequence of MetAP1; MetAP2 is highly conserved between S. cerevisiae and humans. In ...
*  Deletion (genetics)
Other computation methods were selected to discover DNA sequencing deletion errors such as end-sequence profiling. Indel ... In contrast, a deletion that is evenly divisible by three is called an in-frame deletion. Deletions are responsible for an ... In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic ... Types of deletion include the following: 'Terminal Deletion' - a deletion that occurs towards the end of a chromosome. ...
*  Frameshift mutation
The earlier in the sequence the deletion or insertion occurs, the more altered the protein. A frameshift mutation is not the ... The nucleotide sequence of the suspected gene is provided from published gene sequences or from cloning and sequencing of the ... aligns a protein against a DNA sequence allowing frameshifts and introns FastY - compare a DNA sequence to a protein sequence ... Using this method, up to 17 gigabases can be sequenced at once, as opposed to limited ranges for Sanger sequencing of only ...
*  Glossary of genetics
The earlier in the sequence the deletion or insertion occurs, the more altered the final gene product. Contents: Top 0-9 A B C ... The term refers to both the sequence as it exists within a DNA molecule and to the corresponding sequence in RNA transcripts. ... frameshift mutation A mutation caused by insertions or deletions of a number of nucleotides in a nucleic acid sequence that is ... DNA sequencing dominant double helix duplication Contents: Top 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z ...
*  List of MeSH codes (G13)
... sequence deletion MeSH G13.920.590.762.180 --- chromosome deletion MeSH G13.920.590.762.320 --- gene deletion MeSH G13.920. ... sequence homology, amino acid MeSH G13.810.550 --- sequence homology, nucleic acid MeSH G13.810.550.830 --- synteny MeSH ... chromosome deletion MeSH G13.920.590.060 --- base pair mismatch MeSH G13.920.590.120 --- codon, nonsense MeSH G13.920.590.175 ... chromosome deletion MeSH G13.920.590.175.420 --- inversion, chromosome MeSH G13.920.590.175.430 --- isochromosomes MeSH G13.920 ...
*  List of MeSH codes (G05)
... sequence deletion MeSH G05.600.800.180 --- chromosome deletion MeSH G05.600.800.320 --- gene deletion MeSH G05.600.810 --- ...
*  Z-DNA
In mammalian cells, the presence of such sequences was found to produce large genomic fragment deletions due to chromosomal ... A study on Escherichia coli found that gene deletions spontaneously occur in plasmid regions containing Z-DNA-forming sequences ... 1989). "Z-DNA-forming sequences are spontaneous deletion hot spots". Proceedings of the National Academy of Sciences of the ... 2006). "Z-DNA-forming sequences generate large-scale deletions in mammalian cells". The National Academy of Sciences. 108 (8): ...
*  Opitz G/BBB syndrome
In the sequence analysis a positive result would detect 15-50% of the DNA sequence mutated, while a deletion/duplication ... Two different tests can be performed: sequence analysis and deletion/duplication analysis. ... This group includes several other diseases that all result because of a small deletion of chromosome 22 at the q11.2 location. ... Some researchers consider Opitz G/BBB syndrome to be a type of 22q11.2 deletion syndrome (a slightly different and broader ...
*  Conserved signature indels
"Conserved Inserts and Deletions in Protein Sequences". Bacterial Phylogeny. Gupta RS. Retrieved 2 April 2012. [unreliable ... A 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16 were found uniquely in various species ... Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for ... Archaea), it can be inferred whether the indel is an insert or a deletion, and which of these two groups A, B, C or X, Y, Z is ...
*  Human Genome Structural Variation
These repeated sequences could cause deletions, duplications, inversions, and inverted duplication chromosomes. The products of ... When DNA sequencing was introduced, it opened the door to finding smaller and incredibly more sequence variations including ... They decided to sequence 130 breakpoints from 112 individuals that contained 119 known CNVs by doing whole genome sequencing as ... They used sequencing technologies to sequence breakpoint areas of many rare pathogenic copy number variants which was the ...
*  Mung bean nuclease
Unidirectional deletion of large DNA (in combination with Exonuclease III) to generate ordered deletions for sequencing. ... Its ability to recognise double-stranded nucleic acids depends on the base sequence. It tends to cleave at ApN and at T(U) pN. ... Excision of gene coding sequences from genomic DNA. Molecular and Cellular Biology portal. ...
*  Dot plot (bioinformatics)
Insertions and deletions between sequences give rise to disruptions in this diagonal. Regions of local similarity or repetitive ... Note, that the sequences can be written backwards or forwards, however the sequences on both axes must be written in the same ... Dot plots compare two sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When the ... a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16: 1-11. doi:10.1111/j. ...
*  Proteolipid protein 1
Simons R, Alon N, Riordan JR (1987). "Human myelin DM-20 proteolipid protein deletion defined by cDNA sequence". Biochem. ... cloning and sequencing of human proteolipid protein cDNA". J. Neurosci. Res. 18 (3): 395-401. doi:10.1002/jnr.490180303. PMID ...
*  Mutation
The earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is. For example, the code ... Molecular sequence analysis: With rapid development of DNA sequencing technology, an enormous amount of DNA sequence data is ... For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been ... Interstitial deletions: an intra-chromosomal deletion that removes a segment of DNA from a single chromosome, thereby apposing ...
*  IGHG3
... cDNA sequence supports partial gene deletion model". Proc Natl Acad Sci U S A. 79 (10): 3260-4. doi:10.1073/pnas.79.10.3260. ... 1986). "Sequence of a human immunoglobulin gamma 3 heavy chain constant region gene: comparison with the other human C gamma ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Wolfenstein-Todel C, Frangione B, Prelli F, Franklin EC (1976). "The amino acid sequence of "heavy chain disease" protein ZUC. ...
*  Gluten immunochemistry
... strains and isoforms may vary because of insertions and deletions in sequence. There are a large number of wheat variants, and ... These proteins are called MHC class I polypeptide-related sequence A and B. Discovered by sequence homology analysis these ... These proteins once identified and sequenced can be surveyed by sequence homology searches. HLA-DQ recognition of gliadin is ... The sequence of the insert is P-Q-P-Q-L-P-Y-P-Q-P-Q-L-P-Y PMID 10684852 1 "α-I" site, 3 "α-II" sites, and 2 "α-III" sites, PMID ...
*  HBE1
... sequence requirements determined by deletion analysis of an intervening sequence". Proc. Natl. Acad. Sci. U.S.A. 82 (9): 2885-9 ... I. Nucleotide sequences derived from complementary RNA". J. Biol. Chem. 252 (14): 5019-31. PMID 873928. Gelinas R, Endlich B, ... "Entrez Gene: HBE1 hemoglobin, epsilon 1". Clegg JB (1982). "Embryonic hemoglobin: sequence of the epsilon and zeta chains". Tex ... Engelke DR, Hoener PA, Collins FS (1988). "Direct sequencing of enzymatically amplified human genomic DNA". Proc. Natl. Acad. ...
*  Non-homologous end joining
Repair by MMEJ therefore leads to deletion of the DNA sequence between the microhomologies. Many species of bacteria, including ... Deletion of XRCC4 or LIG4 causes embryonic lethality in mice, indicating that NHEJ is essential for viability in mammals. In ... Li H, Vogel H, Holcomb VB, Gu Y, Hasty P (December 2007). "Deletion of Ku70, Ku80, or both causes early aging without ... For example, Ku localizes to telomeres and its deletion leads to shortened telomeres. Ku is also required for subtelomeric ...
*  Ancestral reconstruction
For example, the reconstruction of sequence insertions and deletions (indels) has lagged behind the more straightforward ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... Since modern genetic sequences are essentially a variation of ancient ones, access to ancient sequences may identify other ... This allowed them to hypothesize a phylogeny for the sequences, and to infer that the standard sequence was probably also the ...
*  Phylogenetic footprinting
It is not obvious if these sequences with insertions or deletions are still functional. Though they may still be functional if ... considering insertions and deletions in the sequence would detect a few more true TFBSs, but it could likely include many more ... Align the sequences. Look for conserved regions and analyse them. Not all transcription binding sites can be found using ... These motifs could be detected if sequences from more organisms are available. So this will be less of a problem in the future ...
*  HOXD8
This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...