The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections
Open accessAbstract
High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html.
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Cites
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“The selected biomolecules find application as reagents for diagnostics 1 and therapeutics, 2 and as research tools to probe sequence-structure or sequence-function relationships, 3 fitness landscapes, 4–6 the origins of life, 7 and other questions.”
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Cited by
SELEX: Critical factors and optimization strategies for successful aptamer selection
Kohlberger, M., & Gadermaier, G. (2022) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.2244 · Cited by 341
Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application
Adachi, T., & Nakamura, Y. (2019) · Molecules · doi:10.3390/molecules24234229 · Cited by 300
An RNA toolbox for cancer immunotherapy
Pastor, F., Berraondo, P., Etxeberria, I., Frederick, J., Sahin, U., Gilboa, E., & Melero, I. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.132 · Cited by 229
Di Gioacchino, A., Procyk, J., Molari, M., Schreck, J. S., Zhou, Y., Liu, Y., Monasson, R., Cocco, S., & Šulc, P. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010561 · Cited by 45
DNA aptamer AptERA 2 targets ERA from Staphylococcus aureus and limits GTP hydrolysis
Peñaranda, K., Pereira, N., Savva, O., Petrelli, D., Spurio, R., Corrigan, R. M., & Milon, P. (2025) · Scientific Reports · doi:10.1038/s41598-025-15180-9 · Cited by 2
Metadata
- Authors
- Alam, K. K., Chang, J. L., & Burke, D. H.
- Venue
- Molecular Therapy - Nucleic Acids
- Publisher
- Elsevier BV
- Published
- 2015
- Volume
- 4
- Pages
- e230
- ISSN
- 2162-2531 (ISSN-L)
- OpenAlex
- W2050271637
- Cited by
- 260
- References
- 43
- FWCI
- 7.98
- Type
- journal article
- Language
- en
- Open access
- gold
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