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Brinkmann Instruments tide algorithm
Tide Algorithm, supplied by Brinkmann Instruments, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/tide+algorithm/algorithm+tide/bio_rxiv__64898__2026__01__29__702672-62-7-10
Average 86 stars, based on 1 article reviews
tide algorithm - by Bioz Stars, 2026-10
86/100 stars

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Sequencing:

Article Title: Crystal structure of the CDK11 kinase domain bound to the small molecule inhibitor OTS964
Article Snippet: .. Sequencing chromatograms were assessed for editing using the TIDE algorithm ( Brinkman et al. 2014 ). ..

Article Title: Ibrutinib Blocks YAP1 Activation and Reverses BRAF Inhibitor Resistance in Melanoma Cells.
Article Snippet: .. The Sanger sequencing traces were subsequently deconvoluted with the TIDE algorithm (Brinkman et al., 2014) to identify the fraction of cells that had functional knockout (Fig. 2A; Supplemental Fig. 10). ..

Article Title: Ornithine decarboxylase  genes contribute to S-RNase-independent pollen rejection
Article Snippet: .. Analysis of the ODC2 sequence traces in the transgenic IL 3-3 lines using the TIDE algorithm ( Brinkman et al., 2014 ) showed that each of the independent transformants retained some proportion of WT ODC2 sequences, especially the two T 2 progeny of odc2-3 line which retained >30% of WT ODC2 genotype. ..

Article Title: Comparison of human PEX knockout cell lines suggests a dual role of PEX1 in peroxisome biogenesis.
Article Snippet: From clones showing an import defect or absence of peroxisomal membranes genomic DNAwas isolated using the kit NucleoSpin Tissue (Macherey-Nagel), according to the manufacturer’s instructions. .. The exon with expected double strand break was then PCR-amplified using the Terra PCR Direct Polymerase Mix (Takara) and compared to the wild-type sequence by the TIDE algorithm (Brinkman et al. 2014). ..


Article Title: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice.
Article Snippet: .. www.genome.org S4) using the CRISPOR algorithm (Haeussler et al. 2016) and were synthetized (Synthego). sgRNA were tested for activity by lipofection (RNAiMax, Invitrogen) into a mouse melanocyte cell line (B16F10), pre-engineered to stably express the Cas9 nuclease, followed by incubation for 48 h, and then pooled genomic DNA was assessed for the presence of indel mutations by Sanger sequencing and quantified using the tracking of indels by decomposition (TIDE) algorithm (Brinkman et al. 2014). ..

Mutagenesis:

Article Title: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice.
Article Snippet: .. An assessment of the degree of mutagenesis was performed using the TIDE algorithm (Brinkman et al. 2014). ..

Functional Assay:

Article Title: Ibrutinib Blocks YAP1 Activation and Reverses BRAF Inhibitor Resistance in Melanoma Cells.
Article Snippet: .. The Sanger sequencing traces were subsequently deconvoluted with the TIDE algorithm (Brinkman et al., 2014) to identify the fraction of cells that had functional knockout (Fig. 2A; Supplemental Fig. 10). ..

Knock-Out:

Article Title: Ibrutinib Blocks YAP1 Activation and Reverses BRAF Inhibitor Resistance in Melanoma Cells.
Article Snippet: .. The Sanger sequencing traces were subsequently deconvoluted with the TIDE algorithm (Brinkman et al., 2014) to identify the fraction of cells that had functional knockout (Fig. 2A; Supplemental Fig. 10). ..

Transgenic Assay:

Article Title: Ornithine decarboxylase  genes contribute to S-RNase-independent pollen rejection
Article Snippet: .. Analysis of the ODC2 sequence traces in the transgenic IL 3-3 lines using the TIDE algorithm ( Brinkman et al., 2014 ) showed that each of the independent transformants retained some proportion of WT ODC2 sequences, especially the two T 2 progeny of odc2-3 line which retained >30% of WT ODC2 genotype. ..

Polymerase Chain Reaction:

Article Title: Comparison of human PEX knockout cell lines suggests a dual role of PEX1 in peroxisome biogenesis.
Article Snippet: From clones showing an import defect or absence of peroxisomal membranes genomic DNAwas isolated using the kit NucleoSpin Tissue (Macherey-Nagel), according to the manufacturer’s instructions. .. The exon with expected double strand break was then PCR-amplified using the Terra PCR Direct Polymerase Mix (Takara) and compared to the wild-type sequence by the TIDE algorithm (Brinkman et al. 2014). ..

Activity Assay:

Article Title: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice.
Article Snippet: .. www.genome.org S4) using the CRISPOR algorithm (Haeussler et al. 2016) and were synthetized (Synthego). sgRNA were tested for activity by lipofection (RNAiMax, Invitrogen) into a mouse melanocyte cell line (B16F10), pre-engineered to stably express the Cas9 nuclease, followed by incubation for 48 h, and then pooled genomic DNA was assessed for the presence of indel mutations by Sanger sequencing and quantified using the tracking of indels by decomposition (TIDE) algorithm (Brinkman et al. 2014). ..

Stable Transfection:

Article Title: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice.
Article Snippet: .. www.genome.org S4) using the CRISPOR algorithm (Haeussler et al. 2016) and were synthetized (Synthego). sgRNA were tested for activity by lipofection (RNAiMax, Invitrogen) into a mouse melanocyte cell line (B16F10), pre-engineered to stably express the Cas9 nuclease, followed by incubation for 48 h, and then pooled genomic DNA was assessed for the presence of indel mutations by Sanger sequencing and quantified using the tracking of indels by decomposition (TIDE) algorithm (Brinkman et al. 2014). ..

Incubation:

Article Title: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice.
Article Snippet: .. www.genome.org S4) using the CRISPOR algorithm (Haeussler et al. 2016) and were synthetized (Synthego). sgRNA were tested for activity by lipofection (RNAiMax, Invitrogen) into a mouse melanocyte cell line (B16F10), pre-engineered to stably express the Cas9 nuclease, followed by incubation for 48 h, and then pooled genomic DNA was assessed for the presence of indel mutations by Sanger sequencing and quantified using the tracking of indels by decomposition (TIDE) algorithm (Brinkman et al. 2014). ..



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