AmpliconDesign – an interactive web server for the design of high-throughput targeted DNA methylation assays
| Autor: | Jana Hess, Daniel B. Lipka, Joschka Hey, Yassen Assenov, Pascal Bawidamann, Jens Langstein, Sina Stäble, Dieter Weichenhan, Pavlo Lutsik, Maximilian Schönung |
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| Rok vydání: | 2020 |
| Předmět: |
Epigenomics
0301 basic medicine Cancer Research Web server Source code Computer science media_common.quotation_subject Bisulfite sequencing Computational biology Biology computer.software_genre Polymerase Chain Reaction DNA sequencing Market fragmentation 03 medical and health sciences 0302 clinical medicine Sulfites Epigenetics Binding site Molecular Biology Throughput (business) media_common Brief Report High-Throughput Nucleotide Sequencing Sequence Analysis DNA DNA Methylation Amplicon genomic DNA Biomarker ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology 030220 oncology & carcinogenesis DNA methylation Pyrosequencing Primer (molecular biology) computer Software |
| Zdroj: | Epigenetics |
| ISSN: | 1559-2308 1559-2294 |
| DOI: | 10.1080/15592294.2020.1834921 |
| Popis: | Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq), EpiTYPER MassArray, or pyrosequencing. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq.Availability and ImplementationThe AmpliconDesign webserver is freely available online at: https://amplicondesign.dkfz.de/. AmpliconDesign has been implemented using the R Shiny framework (Chang et al., 2018). The source code is publicly available under the GNU General Public License v3.0 (https://github.com/MaxSchoenung/AmpliconDesign).ContactDaniel B. Lipka (d.lipka@dkfz.de) & Maximilian Schönung (m.schoenung@dkfz.de) |
| Databáze: | OpenAIRE |
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