Results 261 to 270 of about 177,651 (293)

Enabling tandem repeat sequence genotype analysis across capture kits.

Journal of Clinical Oncology, 2022
e18700 Background: Previous studies on mutation calling have documented capture kit batch effects in Whole Exome Sequencing (WES) data from The Cancer Genome Atlas (TCGA) database, hindering direct comparison between samples from different capture kits. For example, in classification, a cancer type exclusively sampled by a specific capture kit in the
Shun H Yip, Michael Diamreyan, Edmund Wong, Raghuraman Ramamurthy, Sidney Tobias, Hao Cheng, Victor Solovyev, Cheuk Ying Tang   +7 more
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Tandem repeats in proteins: From sequence to structure

Journal of Structural Biology, 2012
The bioinformatics analysis of proteins containing tandem repeats requires special computer programs and databases, since the conventional approaches predominantly developed for globular domains have limited success. Here, I survey bioinformatics tools which have been developed recently for identification and proteome-wide analysis of protein repeats ...
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Short tandem repeat sequencing on the 454 platform

Forensic Science International: Genetics Supplement Series, 2011
Abstract To investigate the feasibility of next generation sequencing (NGS) technology for the multiplex detection and sequence production of short tandem repeats (STRs), thirteen STR markers (CSF1PO, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D13S317, D16S539, D21S11, D22S1045, TPOX, and vWA) were amplified using an optimized multiplex ...
Melissa Scheible, Odile Loreille, Rebecca Just, Jodi Irwin   +3 more
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Greedily assemble tandem repeats for next generation sequences

International Journal of High Performance Computing and Networking, 2019
Eukaryotic genomes contain high volumes of intronic and intergenic regions in which repetitive sequences are abundant. These repetitive sequences represent challenges in genomic assignment of short read sequences generated through next generation sequencing and are often excluded in analysis losing invaluable genomic information.
Yongqing Jiang, Jinhua Lu, Jingyu Hou, Wanlei Zhou   +3 more
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Locating Tandem Repeats in Weighted Biological Sequences

2012
A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to locate all the tandem repeats in a weighted sequence. By introducing the idea of equivalence classes in weighted sequences, we identify the tandem repeats of every possible length using an ...
Hui Zhang, Qing Guo, Costas S. Iliopoulos   +2 more
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Detection and visualization of tandem repeats in dna sequences

IEEE Transactions on Signal Processing, 2003
One conspicuous feature of DNA is the extent to which nucleotide subsequences repeat in the genome. Several strongly repetitive tandem (or contiguous) repeats are known to be associated with genetic diseases, while weaker repetitive structures are thought to be representative of historical events associated with sequence repetition.
M. Buchner, S. Janjarasjitt
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Sequencing and characterizing short tandem repeats in the human genome

Nature Reviews Genetics
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height.
Hope A. Tanudisastro, Ira W. Deveson, Harriet Dashnow, Daniel G. MacArthur   +3 more
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Forensic nomenclature for short tandem repeats updated for sequencing

Forensic Science International: Genetics Supplement Series, 2015
Abstract The introduction of massively parallel sequencing (MPS) techniques enables sequencing of short tandem repeats (STR) as a new tool for forensic research. In addition to variation in fragment-length, MPS also reveals allelic sequence-variation in STR-fragments. This additional variation demands a new way of describing allelic variants.
Kristiaan J. van der Gaag, Peter de Knijff   +1 more
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Differences and similarities between various tandem repeat sequences: Minisatellites and microsatellites

Biochimie, 1997
Tandemly repetitive DNA sequences are abundantly interspersed in the genome of practically all eukaryotic species studied. The relative occurrence of one type of repetitive sequence and its location in the genome appear to be species specific. A common property of repetitive sequences within the living world is their ability to give rise to variants ...
H, Debrauwere, C G, Gendrel, S, Lechat, M, Dutreix   +3 more
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Nucleotide sequence of the Urechis caupo core histone gene tandem repeat

DNA Sequence, 1992
The 4942 bp nucleotide sequence of a repeating unit from the core histone gene tandem repeat of Urechis caupo and the predicted amino acid sequence of the four core histones are presented. Putative promoter elements including the CAP site and TATA box as well as multiple CAAT-like sequences are identified upstream from each gene.
F C, Davis, J C, Shelton, L D, Ingham
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