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Position-based sequence weights
Journal of Molecular Biology, 1994Sequence weighting methods have been used to reduce redundancy and emphasize diversity in multiple sequence alignment and searching applications. Each of these methods is based on a notion of distance between a sequence and an ancestral or generalized sequence.
S, Henikoff, J G, Henikoff
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Pattern Based Sequence Classification
IEEE Transactions on Knowledge and Data Engineering, 2016Sequence classification is an important task in data mining. We address the problem of sequence classification using rules composed of interesting patterns found in a dataset of labelled sequences and accompanying class labels. We measure the interestingness of a pattern in a given class of sequences by combining the cohesion and the support of the ...
Zhou, Cheng, Cule, Boris, Goethals, Bart
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Itemset Based Sequence Classification
2013Sequence classification is an important task in data mining. We address the problem of sequence classification using rules composed of interesting itemsets found in a dataset of labelled sequences and accompanying class labels. We measure the interestingness of an itemset in a given class of sequences by combining the cohesion and the support of the ...
Zhou, Cheng, Cule, Boris, Goethals, Bart
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2015
Marker-assisted selection (MAS) has revolutionized plant and animal breeding activities. MAS is based on DNA markers, which facilitate gene/QTL identification and mapping and gene/QTL transfer, and has many other applications. Some of the important issues concerning marker systems relate to their abundance, genome-wide distribution, cost and effort for
B. D. Singh, A. K. Singh
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Marker-assisted selection (MAS) has revolutionized plant and animal breeding activities. MAS is based on DNA markers, which facilitate gene/QTL identification and mapping and gene/QTL transfer, and has many other applications. Some of the important issues concerning marker systems relate to their abundance, genome-wide distribution, cost and effort for
B. D. Singh, A. K. Singh
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Sequencing-based analysis of microbiomes
Nature Reviews GeneticsMicrobiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA
Yishay Pinto, Ami S. Bhatt
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Skim-Based Genotyping by Sequencing
2014Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of individuals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the individual study design GBS protocols can take multiple forms, however most share a sequence ...
Golicz, Agnieszka A. +2 more
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Consistency of Sequence-Based Gene Clusters
Journal of Computational Biology, 2010In comparative genomics, differences or similarities of gene orders are determined to predict functional relations of genes or phylogenetic relations of genomes. For this purpose, various combinatorial models can be used to specify gene clusters--groups of genes that are co-located in a set of genomes.
Wittler, Roland +3 more
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Sequencing-Based Typing of HLA
2007Human leukocyte antigen (HLA) typing is largely performed by use of PCR-based techniques in patients that require stem cell transplantation. In this chapter, HLA typing by sequencing-based typing techniques is described.
Berthold, Hoppe, Abdulgabar, Salama
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Moving towards sequencing-based metabolomics
Trends in GeneticsMetabolites are chemically heterogeneous and difficult to quantify in easily read formats. Recently, Tan and Fraser demonstrated that metabolites can be readily quantified by pairing aptamer function with DNA sequencing. This reflects a larger trend of sequencing for assessing biomolecule abundances, further leading to sequencing being a universal ...
Alia Clark-ElSayed +2 more
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Journal of Molecular Biology, 1964
Nucleotide sequences have been studied in pancreatic RNase digests of soluble RNA. Various sequences containing “odd” nucleotides have been identified. The finding of sequences with more than one “odd” nucleotide, such as 2-dimethyl guanyl-5-ribosyl uracil phosphate and 1-methyl guanyl-2-methyl guanyl cytidylic acid, is evidence for a clustering of the
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Nucleotide sequences have been studied in pancreatic RNase digests of soluble RNA. Various sequences containing “odd” nucleotides have been identified. The finding of sequences with more than one “odd” nucleotide, such as 2-dimethyl guanyl-5-ribosyl uracil phosphate and 1-methyl guanyl-2-methyl guanyl cytidylic acid, is evidence for a clustering of the
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