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AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX

Kevin R. Shieh, Christina Kratschmer, Keith E. Maier, John M. Greally, Matthew Levy, Aaron Golden
doi: https://doi.org/10.1101/413757
Kevin R. Shieh
Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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Christina Kratschmer
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
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Keith E. Maier
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
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John M. Greally
Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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Matthew Levy
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
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Aaron Golden
Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USASchool of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland
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ABSTRACT

Summary: High-Throughput Sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment (HTS-SELEX). Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. Whilst several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI- enabled environment. We demonstrate AptCompare’s performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences’ rankings and their binding affinities.

Availability and Implementation: The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 12, 2018.
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AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
Kevin R. Shieh, Christina Kratschmer, Keith E. Maier, John M. Greally, Matthew Levy, Aaron Golden
bioRxiv 413757; doi: https://doi.org/10.1101/413757
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AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
Kevin R. Shieh, Christina Kratschmer, Keith E. Maier, John M. Greally, Matthew Levy, Aaron Golden
bioRxiv 413757; doi: https://doi.org/10.1101/413757

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