FASTAptameR 2.0: A web tool for combinatorial sequence selections

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

doi:10.1016/j.omtn.2022.08.030

Cited by 15 publications

(17 citation statements)

References 72 publications

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“…We next compared the capabilities and output of AptamerRunner to the capabilities and output of FASTAptamer, FASTAptameR 2.0 and AptaCluster (22-24,34). Details and features of FASTAptamer, FASTAptameR 2.0, AptaCluster and AptamerRunner are summarized in Table 1 .…”

Section: Resultsmentioning

confidence: 99%

“…The cluster module and diversity module of FASTAptameR 2.0 (6) were run using the same counted FASTA input file as used with FASTAptamer-Cluster. The FASTAptameR 2.0 cluster module was run with edit distance 1 with the number of clusters set to maximum.…”

Section: Supplemental Methodsmentioning

confidence: 99%

“…However, this early clustering algorithm was not easily accessible and thus has not been widely adopted. The current prevailing clustering algorithms include AptaCluster (21,22), FASTAptamer (23), and FASTAptameR 2.0 (24). These tools generate networks of related aptamers using either Hamming or Levenshtein edit distance and introduced a new concept for clustering aptamers termed the seed approach .…”

Section: Introductionmentioning

confidence: 99%

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AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Ruiz-Ciancio,

Veeramani,

Embree

et al. 2023

Preprint

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Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.GRAPHICAL ABSTRACT

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Section: Resultsmentioning

confidence: 99%

Section: Supplemental Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Ruiz-Ciancio,

Veeramani,

Embree

et al. 2023

Preprint

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“…More than 34 million high-quality reads remained following data preprocessing to merge paired end reads, trim off constant regions, and remove low quality or ambiguous reads. Processed libraries were analyzed using the FASTAptamer toolkit ( 47 ) and its R-based reimplementation, FASTAptameR 2.0 ( 48 ). Read counts and the number of unique aptamer sequences for each library are shown in Table S1.…”

Section: Resultsmentioning

confidence: 99%

“…Processed populations were then analyzed using FASTAptamer software ( 47 ) and its R-based re-implementation FASTAptameR 2.0 ( 48 ) to count and normalize reads (FASTAptameR-Count), calculate fold enrichment and compare populations (FASTAptameR-Sequence Enrichment), group related sequences together (FASTAptameR-Cluster), analyze cluster composition (FASTAptameR-Cluster Diversity), and calculate fold enrichment of clusters (FASTAptameR-Cluster Enrichment).…”

Section: Methodsmentioning

confidence: 99%

Differentiation SELEX approach identifies RNA aptamers with different specificities for HIV-1 capsid assembly forms

Gruenke,

Mayer,

Aneja

et al. 2023

Preprint

Self Cite

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The HIV-1 capsid protein (CA) assumes distinct assembly forms during replication, each presenting unique, solvent-accessible surfaces that facilitate multifaceted functions and host factor interactions. However, contributions of individual CA assemblies remain unclear, as the evaluation of CA in cells presents several technical challenges. To address this need, we sought to identify CA assembly form-specific aptamers. Aptamer subsets with different specificities emerged from within a highly converged, pre-enriched aptamer library previously selected to bind the CA hexamer lattice. Subsets were either highly specific for CA lattice or bound both CA lattice and CA hexamer. We further evaluated four representatives to reveal aptamer structural features required for binding, highlighting interesting features and challenges in aptamer structure determination. Importantly, our aptamers bind biologically relevant forms of CA and we demonstrate aptamer-mediated affinity purification of CA from cell lysates without virus or host modification. Thus, we have identified CA assembly form-specific aptamers that represent exciting new tools for the study of CA.

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Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

Bian,

Pei,

Gao

et al. 2024

Adv Healthcare Materials

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Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.

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FASTAptameR 2.0: A web tool for combinatorial sequence selections

Cited by 15 publications

References 72 publications

AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Differentiation SELEX approach identifies RNA aptamers with different specificities for HIV-1 capsid assembly forms

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

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