Peng Jiang1, Susanne Meyer1, Zhonggang Hou1, Nicholas E Propson1, H Tom Soh1, James A Thomson2, Ron Stewart1. 1. Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA. 2. Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
Abstract
UNLABELLED: Aptamers are 'synthetic antibodies' that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict the BIND: ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis. AVAILABILITY AND IMPLEMENTATION: MPBind software and documents are available at http://www.morgridge.net/MPBind.html. The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/.
UNLABELLED: Aptamers are 'synthetic antibodies' that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict the BIND: ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis. AVAILABILITY AND IMPLEMENTATION: MPBind software and documents are available at http://www.morgridge.net/MPBind.html. The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/.
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