FASTAptameR 2.0: A web tool for combinatorial sequence selections

Skyler T Kramer; Paige R Gruenke; Khalid K Alam; Dong Xu; Donald H Burke

doi:10.1016/j.omtn.2022.08.030

FASTAptameR 2.0: A web tool for combinatorial sequence selections

Mol Ther Nucleic Acids. 2022 Aug 24:29:862-870. doi: 10.1016/j.omtn.2022.08.030. eCollection 2022 Sep 13.

Authors

Skyler T Kramer^{1

2}, Paige R Gruenke^{2

3}, Khalid K Alam⁴, Dong Xu^{1

2

5}, Donald H Burke^{2

3

6}

Affiliations

¹ MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
² Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
³ Department of Biochemistry, University of Missouri School of Medicine, Columbia, MO, USA.
⁴ Stemloop, Inc., Evanston, IL 60201, USA.
⁵ Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
⁶ Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, USA.

Abstract

Combinatorial selections are powerful strategies for identifying biopolymers with specific biological, biomedical, or chemical characteristics. Unfortunately, most available software tools for high-throughput sequencing analysis have high entrance barriers for many users because they require extensive programming expertise. FASTAptameR 2.0 is an R-based reimplementation of FASTAptamer designed to minimize this barrier while maintaining the ability to answer complex sequence-level and population-level questions. This open-source toolkit features a user-friendly web tool, interactive graphics, up to 100 times faster clustering, an expanded module set, and an extensive user guide. FASTAptameR 2.0 accepts diverse input polymer types and can be applied to any sequence-encoded selection.

Keywords: MT: Bioinformatics; Next-generation sequencing; SELEX; aptamer; combinatorial selection; directed evolution; phage display; ribozyme; sequence analysis; synthetic biology.