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Jagannathan V, Roulet E, Delorenzi M, Bucher P. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D90-4. PMID:12101405 High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. A highly multiplexed, parallel HT-SELEX method was developed for NGS (Jolma et al., 2010). A variation of SELEX-seq (Slattery et al., 2011) uses Nextera adapter sequences for efficient library preparation (Zhang et al., 2016). In this work we identify by HT-SELEX TIM3 non-antigenic oligonucleotide aptamers (TIM3Apt) that bind with high affinity and specificity to the extracellular motives of TIM3 on the cell surface.

Ht selex

SELEX (systematic evolution of ligands by exponential enrichment) was created 20 years ago as a method to enrich small populations of bound DNAs from a random sequence pool by PCR amplification. It provides a powerful way to determine the in vitro binding specificities of DNA-binding proteins such as transcription factors. High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. Currently available clustering methods for HT-SELEX only estimate clusters based on the similarity of full-length sequences or limited length of motifs as target binding regions. Hence, a clustering method considering the target binding region with different lengths is required.

8 In this method, proteins are expressed as fusions with streptavidin-binding peptide (SBP), conjugated to Gaussia luciferase, in the pD40htSELEX expression vector.

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Recently developed high-throughput experimental methods, including protein binding microarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the specificities for hundreds of TFs. However, few studies have developed efficient algorithms for estimating binding motifs based on HT-SELEX data. The emergence of High Throughput SELEX (HT-SELEX) has opened the eld to new computational oppor- tunities and challenges that are yet to be addressed.

The emergence of High Throughput SELEX (HT-SELEX) has opened the eld to new computational oppor- tunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selec- tion process itself, we developed AptaCluster. AptaSUITE is a platform independent implementation of multiple algorithms designed for the identification of aptamer candidate sequences and the analysis of the SELEX process per se. It provides both, command line and graphical user interfaces. The HTPSELEX database contains sets of invitro selected transcription factor binding site sequences obtained with SELEX and high-throughput SELEX method. The database hosts 12 individual Selex libraries for the transcription factors CTF/NF1 and LEF/TCF families totaling more than 40,000 sites. High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies.
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This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for HT-SELEX is an in vitro experimental method that improves the conventional SELEX method (21, 22) by including next generation sequencing (NGS) technology so that a larger amount of nucleotide sequence information can be processed. 2017-09-21 · 1. PLoS One. 2017 Sep 21;12(9):e0185169.

Hoinka J(1), Przytycka T(2). Author information: (1)National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions.
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We have developed FSBC method for HT-SELEX data implemented in R. FSBC exhibited the highest accuracy of sequence clustering compared with conventional methods, w In this work we identify by HT-SELEX TIM3 non-antigenic oligonucleotide aptamers (TIM3Apt) that bind with high affinity and specificity to the extracellular motives of TIM3 on the cell surface. HT-SELEX protocol. Our model takes into account the factthatateachcycle,thesequencedaptamersonlyrepre-sentafractionofthetruepoolsize(Figure1b).

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