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MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

MOTIVATION: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-...

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Autores principales: Georgakopoulos-Soares, Ilias, Jain, Naman, Gray, Jesse M, Hemberg, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198521/
https://www.ncbi.nlm.nih.gov/pubmed/27605100
http://dx.doi.org/10.1093/bioinformatics/btw584
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author Georgakopoulos-Soares, Ilias
Jain, Naman
Gray, Jesse M
Hemberg, Martin
author_facet Georgakopoulos-Soares, Ilias
Jain, Naman
Gray, Jesse M
Hemberg, Martin
author_sort Georgakopoulos-Soares, Ilias
collection PubMed
description MOTIVATION: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. RESULTS: We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences, thereby allowing the investigation of the rules that govern transcription factor (TF) occupancy. MPRA single-nucleotide polymorphism design can be used to systematically examine the functional effects of single or combinations of single-nucleotide polymorphisms at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs. AVAILABILITY AND IMPLEMENTATION: MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator. The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. The REST API allows programmatic access to MPRAnator using simple URLs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-51985212017-01-06 MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments Georgakopoulos-Soares, Ilias Jain, Naman Gray, Jesse M Hemberg, Martin Bioinformatics Applications Notes MOTIVATION: With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as massively parallel reporter assays (MPRAs) and similar methods remains challenging. RESULTS: We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences, thereby allowing the investigation of the rules that govern transcription factor (TF) occupancy. MPRA single-nucleotide polymorphism design can be used to systematically examine the functional effects of single or combinations of single-nucleotide polymorphisms at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs. AVAILABILITY AND IMPLEMENTATION: MPRAnator tool set is implemented in Python, Perl and Javascript and is freely available at www.genomegeek.com and www.sanger.ac.uk/science/tools/mpranator. The source code is available on www.github.com/hemberg-lab/MPRAnator/ under the MIT license. The REST API allows programmatic access to MPRAnator using simple URLs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-01-01 2016-09-06 /pmc/articles/PMC5198521/ /pubmed/27605100 http://dx.doi.org/10.1093/bioinformatics/btw584 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Georgakopoulos-Soares, Ilias
Jain, Naman
Gray, Jesse M
Hemberg, Martin
MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title_full MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title_fullStr MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title_full_unstemmed MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title_short MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
title_sort mpranator: a web-based tool for the design of massively parallel reporter assay experiments
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198521/
https://www.ncbi.nlm.nih.gov/pubmed/27605100
http://dx.doi.org/10.1093/bioinformatics/btw584
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