• expressed genes
  • Analysis of the incidence of mononucleotide repeat sequences in the 3'UTRs, 5'UTRs, and coding sequences of those genes most differentially expressed in RER+ versus RER- cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3'UTR T repeats longer than 11 base pairs in the most differentially expressed genes. (ox.ac.uk)
  • Sequence analysis of the 3'UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. (ox.ac.uk)
  • INsertion or DELetion
  • Just by looking at our two strings one may be able to see one possible best alignment: GCATG-CU G-ATTACA One can see that letters may match, mismatch, be deleted or inserted (indel): Match: The two letters are the same Mismatch: The two letters are differential Indel (INsertion or DELetion): One letter aligns to a gap in the other string. (wikipedia.org)
  • Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original. (wikipedia.org)
  • genomic
  • Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci. (aaccjnls.org)
  • Excision of gene coding sequences from genomic DNA. (wikipedia.org)
  • JDotter - Java version of Dotter Dotplot, easy (educational) HTML5 tool to generate dot plots from RNA sequences lastz and laj, programs to prepare and visualize genomic alignments. (wikipedia.org)
  • Similarity
  • Instead of looking at the entire sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure. (wikipedia.org)
  • s ( a , b ) {\displaystyle s(a,b)} - Similarity score of the elements that constituted the two sequences W k {\displaystyle W_{k}} - The penalty of a gap that has length k {\displaystyle k} Construct a scoring matrix H {\displaystyle H} and initialize its first row and first column. (wikipedia.org)
  • For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix. (wikipedia.org)
  • Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. (wikipedia.org)
  • The closeness of the sequences in similarity will determine how close the diagonal line is to what a graph showing a curve demonstrating a direct relationship is. (wikipedia.org)
  • proteins
  • Sequence alignment shows the relations between genes or between proteins, leading to a better understanding of their homology and functionality. (wikipedia.org)
  • Out of nearly 500 known amino acids, a set of 20 are coded for by the standard genetic code and incorporated in sequence as the building blocks of polypeptides and hence proteins. (wikipedia.org)
  • The sequences of amino acids in polypeptide chains that form proteins determine the proteins' structure and function. (wikipedia.org)
  • These were introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. (wikipedia.org)
  • Humans
  • Such deletions in humans are referred to as hCONDELs may be responsible for the anatomical and behavioral differences between humans, chimpanzees and other mammals. (wikipedia.org)
  • Disorders
  • Some medium-sized deletions lead to recognizable human disorders, e.g. (wikipedia.org)
  • Deletions are responsible for an array of genetic disorders, including some cases of male infertility and two thirds of cases of Duchenne muscular dystrophy. (wikipedia.org)
  • Syndrome
  • However, the autosomal dominant cases are also categorized under a more commonly diagnosed group called 22q11.2 deletion syndrome. (wikipedia.org)
  • Some researchers consider Opitz G/BBB syndrome to be a type of 22q11.2 deletion syndrome (a slightly different and broader disease). (wikipedia.org)
  • populations
  • We designed a 159-smMIP panel targeting 40 autosomal regions of frequent homozygous deletion across human populations and 2 sex-linked loci. (aaccjnls.org)
  • organisms
  • By determining the presence or absence of CSIs in an out-group species, one can infer whether the ancestral form of the CSI was an insert or deletion and this can be used to develop a rooted phylogenetic relationship among organisms. (wikipedia.org)
  • algorithm
  • In 1970, Saul B. Needleman and Christian D. Wunsch proposed a heuristic homology algorithm for sequence alignment, also referred to as the Needleman-Wunsch algorithm. (wikipedia.org)
  • It is a global alignment algorithm that requires O ( m n ) {\displaystyle O(mn)} calculation steps ( m {\displaystyle m} and n {\displaystyle n} are the lengths of the two sequences being aligned). (wikipedia.org)
  • The Smith-Waterman algorithm is fairly demanding of time: To align two sequences of lengths m {\displaystyle m} and n {\displaystyle n} , O ( m 2 n ) {\displaystyle O(m^{2}n)} time is required. (wikipedia.org)
  • In 1971, Sankoff became interested in molecular sequence comparison and devised the first quadratic-time variant of the Needleman-Wunsch algorithm for pairwise sequence alignment. (wikipedia.org)
  • regions
  • Low-complexity regions are regions in the sequence with only a few amino acids, which in turn, causes redundancy within that small or limited region. (wikipedia.org)
  • lengths
  • b_{m}} be the sequences to be aligned, where n {\displaystyle n} and m {\displaystyle m} are the lengths of A {\displaystyle A} and B {\displaystyle B} respectively. (wikipedia.org)
  • novel
  • Analysis of the mutant transcripts revealed fusion of the THRA1 exon 7 by splicing to a novel sequence designated BTR for "BT474 transcribed rearrangement. (aacrjournals.org)
  • promoters
  • Only a few isoforms contain the requisite three or more N-terminal zinc motifs that confer high affinity binding to a specific core DNA sequence element in the promoters of target genes. (cancerindex.org)
  • tends
  • The alignment of unrelated sequences tends to produce optimal local alignment scores which follow an extreme value distribution. (wikipedia.org)