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  • 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)
  • 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)
  • 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)
  • 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)
  • proband
  • Pipeline usage in 10 proband family sets revealed a possibly causative deletion SV in the MMP21 gene for two siblings. (ku.edu)
  • 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)
  • 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)
  • The Needleman-Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. (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)
  • 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)
  • possibility
  • The presence of one of these features, or the presence of multiple features, will cause for multiple lines to be plotted in a various possibility of configurations, depending on the features present in the sequences. (wikipedia.org)
  • tends
  • The alignment of unrelated sequences tends to produce optimal local alignment scores which follow an extreme value distribution. (wikipedia.org)
  • alignment
  • Sequence alignment can also reveal conserved domains and motifs. (wikipedia.org)
  • This property allows programs to produce an expectation value for the optimal local alignment of two sequences, which is a measure of how often two unrelated sequences would produce an optimal local alignment whose score is greater than or equal to the observed score. (wikipedia.org)
  • In particular, he had a key role in introducing dynamic programming for sequence alignment and other problems in computational biology. (wikipedia.org)
  • In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ribosomal RNA, laying the algorithmic foundations of comparative genomics. (wikipedia.org)
  • Diagnostic
  • CONCLUSIONS The identification of deletion SVs has the potential to increase the diagnostic yield of WGS data. (ku.edu)
  • small
  • Microdeletion - a relatively small amount of deletion (up to 5Mb that could include a dozen genes). (wikipedia.org)
  • 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)
  • genomes
  • Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the empirically derived correlation, and the ultimate proof of the correlation remains to be obtained by sequencing some of the largest eukaryotic genomes, current data do not seem to rule out a correlation. (wikipedia.org)
  • This involved firstly identifying a subset of 37,251 human deletions(hDELs) through pairwise comparisons of chimpanzee and macaque genomes. (wikipedia.org)
  • Species
  • Biologists can determine and then compare mtDNA sequences among different species and use the comparisons to build an evolutionary tree for the species examined. (wikipedia.org)
  • Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, mouse and chicken sequences with BLASTZ followed by multiple alignment of the pairwise alignments done with MULTIZ. (wikipedia.org)
  • among
  • Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. (wikipedia.org)
  • another
  • As input, the DESeq2 package expects count data as obtained, e.g., from RNA-Seq or another high-throughput sequencing experiment, in the form of a matrix of integer values. (bioconductor.org)
  • single
  • It is important to know if the sequencing experiment was single-end or paired-end, as the alignment software will require the user to specify both FASTQ files for a paired-end experiment. (bioconductor.org)
  • important
  • These represent a new class of regulatory sequences and may have played an important role in the development of specific traits and behavior that distinguish closely related organisms from each other. (wikipedia.org)
  • size
  • The median size of these 510 validated CONDELs is about 2,804 bp thus showing a diverse range in length of the characteristic deletions. (wikipedia.org)