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Academic literature on the topic 'OLIGONUCLEOTIDE FREQUENCIES'

Author: Grafiati
Published: 11 September 2023

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Journal articles on the topic "OLIGONUCLEOTIDE FREQUENCIES"

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Martindale, Colin, and Andrzej K. Konopka. "Oligonucleotide frequencies in DNA follow a Yule distribution." Computers & Chemistry 20, no. 1 (March 1996): 35–38. http://dx.doi.org/10.1016/s0097-8485(96)80005-2.

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Wang, G., D. D. Levy, M. M. Seidman, and P. M. Glazer. "Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation." Molecular and Cellular Biology 15, no. 3 (March 1995): 1759–68. http://dx.doi.org/10.1128/mcb.15.3.1759.

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As an alternative to standard gene transfer techniques for genetic manipulation, we have investigated the use of triple helix-forming oligonucleotides to target mutations to selected genes within mammalian cells. By treating monkey COS cells with oligonucleotides linked to psoralen, we have generated targeted mutations in a simian virus 40 (SV40) vector contained within the cells via intracellular triple helix formation. Oligonucleotide entry into the cells and sequence-specific triplex formation within the SV40 DNA deliver the psoralen to the targeted site. Photoactivation of the psoralen by long-wavelength UV light yields adducts and thereby mutations at that site. We engineered into the SV40 vector novel supF mutation reporter genes containing modified polypurine sites amenable to triplex formation. By comparing the abilities of a series of oligonucleotides to target these new sites, we show that targeted mutagenesis in vivo depends on the strength and specificity of the third-strand binding. Oligonucleotides with weak target site binding affinity or with only partial target site homology were ineffective at inducing mutations in the SV40 vectors within the COS cells. We also show that the targeted mutagenesis is dependent on the oligonucleotide concentration and is influenced by the timing of the oligonucleotide treatment and of the UV irradiation of the cells. Frequencies of intracellular targeted mutagenesis in the range of 1 to 2% were observed, depending upon the conditions of the experiment. DNA sequence analysis revealed that most of the mutations were T.A-to-A.T transversions precisely at the targeted psoralen intercalation site. Several deletions encompassing that site were also seen. The ability to target mutations to selected sites within mammalian cells by using modified triplex-forming oligonucleotides may provide a new research tool and may eventually lead to therapeutic applications.
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3

Hong, Juan. "Prediction of oligonucleotide frequencies based upon dinucleotide frequencies obtained from the nearest neighbor analysis." Nucleic Acids Research 18, no. 6 (1990): 1625–28. http://dx.doi.org/10.1093/nar/18.6.1625.

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Tyagi, Antariksh, Sumit K. Bag, Virendra Shukla, Sribash Roy, and Rakesh Tuli. "Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms." PLoS ONE 5, no. 8 (August 20, 2010): e12330. http://dx.doi.org/10.1371/journal.pone.0012330.

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Goussarov, Gleb, Ilse Cleenwerck, Mohamed Mysara, Natalie Leys, Pieter Monsieurs, Guillaume Tahon, Aurélien Carlier, Peter Vandamme, and Rob Van Houdt. "PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing." Bioinformatics 36, no. 8 (January 3, 2020): 2337–44. http://dx.doi.org/10.1093/bioinformatics/btz964.

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Abstract Motivation One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances. Results Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses. Availability and implementation The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available. Supplementary information Supplementary data are available at Bioinformatics online.
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McFarland, JG, RH Aster, JB Bussel, JG Gianopoulos, RS Derbes, and PJ Newman. "Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele- specific oligonucleotide probes." Blood 78, no. 9 (November 1, 1991): 2276–82. http://dx.doi.org/10.1182/blood.v78.9.2276.2276.

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Abstract The prediction of neonatal alloimmune thrombocytopenia (NATP) in affected families has, in the past, been based on information about gene frequencies of the antigen systems involved, parental phenotyping, and fetal platelet counts. We explored the feasibility of allele- specific oligonucleotide probe typing for PIA antigens to determine the risk of second or subsequent fetuses in families where one infant had a diagnosis of anti-PIA1-mediated NATP. A total of eight families at risk for delivering an affected fetus were studied with both serologic and oligonucleotide typing. The correlation between serologic and oligonucleotide PIA types was 100%. Similarly, in an additional eight families not at risk for PIA1-mediated NATP, serologic and oligonucleotide typing maintained a perfect correlation. DNA isolated from fetal leukocytes as well as fetal amniocytes was successfully typed using this technology. Oligonucleotide-based typing of fetuses at risk for NATP whose fathers are heterozygous for the PIA antigens allows early recognition of affected fetuses so that prenatal therapy of mothers can be instituted if necessary. When fetuses are found to be unaffected, invasive, and/or expensive, prenatal interventions can be avoided.
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McFarland, JG, RH Aster, JB Bussel, JG Gianopoulos, RS Derbes, and PJ Newman. "Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele- specific oligonucleotide probes." Blood 78, no. 9 (November 1, 1991): 2276–82. http://dx.doi.org/10.1182/blood.v78.9.2276.bloodjournal7892276.

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The prediction of neonatal alloimmune thrombocytopenia (NATP) in affected families has, in the past, been based on information about gene frequencies of the antigen systems involved, parental phenotyping, and fetal platelet counts. We explored the feasibility of allele- specific oligonucleotide probe typing for PIA antigens to determine the risk of second or subsequent fetuses in families where one infant had a diagnosis of anti-PIA1-mediated NATP. A total of eight families at risk for delivering an affected fetus were studied with both serologic and oligonucleotide typing. The correlation between serologic and oligonucleotide PIA types was 100%. Similarly, in an additional eight families not at risk for PIA1-mediated NATP, serologic and oligonucleotide typing maintained a perfect correlation. DNA isolated from fetal leukocytes as well as fetal amniocytes was successfully typed using this technology. Oligonucleotide-based typing of fetuses at risk for NATP whose fathers are heterozygous for the PIA antigens allows early recognition of affected fetuses so that prenatal therapy of mothers can be instituted if necessary. When fetuses are found to be unaffected, invasive, and/or expensive, prenatal interventions can be avoided.
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8

Obata, Fumiya, Koichi Ito, Takehisa Kaneko, Yong-guang Yang, Kelji Onda, Ichiro Ito, Noriko Yabe, Koji Watanabo, and Noboru Kashiwagi. "HLA-DR gene frequencies in the Japanese population obtained by oligonucleotide genotyping." Tissue Antigens 38, no. 1 (July 1991): 124–32. http://dx.doi.org/10.1111/j.1399-0039.1991.tb02025.x.

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Abe, Takashi, Yuta Hamano, and Toshimichi Ikemura. "Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis onDrosophilaGenomes." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/985706.

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A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method “BLSOM” for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12Drosophilaspecies, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.
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Bai, Yu, Yuki Iwasaki, Shigehiko Kanaya, Yue Zhao, and Toshimichi Ikemura. "A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data." BioMed Research International 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/765648.

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With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature,” and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).
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Dissertations / Theses on the topic "OLIGONUCLEOTIDE FREQUENCIES"

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PRATIBHA. "DISCRIMINATION OF PATHOGENIC SPECIES USING OLIGONUCLEOTIDE FREQUENCIES OF BARCODING." Thesis, 2016. http://dspace.dtu.ac.in:8080/jspui/handle/repository/14707.

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Now days, molecular taxonomy has become a more targeted tool to classify enormous diversity of the organisms present on earth. As a part of molecular taxonomy DNA based methods especially DNA bar coding serves as a more precise tool for identification and subsequent targeted techniques. The genuses of worms which are chosen are the popular organisms of various human and animal diseases. Currently, only physiological mode of diagnoses is available to detect the type of infection. Our proposed technique works on knowledge based methods of diagnosis where the basis of diagnosis is taken as the whole genome of the organism. The characteristic of this sequence based method is based on the nucleotide indices and DNA bar coding techniques. This technique will help in a more precise and rapid diagnosis. This approach has been extended to other pathogenic organisms for accurate diagnosis and personalized treatment measures. The analytical tool has been developed in JAVA for better user interface and ease of use by researchers. Currently the tool is in offline standalone format but it can also be made an online tool hosted by a server with very minor changes.
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Book chapters on the topic "OLIGONUCLEOTIDE FREQUENCIES"

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Wang, Jia, Chuang Ma, Dao Zhou, Libin Zhang, and Yanhong Zhou. "Accurately Predicting Transcription Start Sites Using Logitlinear Model and Local Oligonucleotide Frequencies." In Bio-Inspired Computing and Applications, 107–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-24553-4_16.

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Conference papers on the topic "OLIGONUCLEOTIDE FREQUENCIES"

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Wu, Hongwei. "PCA-based linear combinations of oligonucleotide frequencies for metagenomic DNA fragment binning." In 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2008). IEEE, 2008. http://dx.doi.org/10.1109/cibcb.2008.4675758.

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