FASTAptameR 2.0: A Web Tool for Combinatorial Sequence Selections

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 opensource toolkit features a user-friendly web tool, interactive graphics, up to 100x 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.

Selection, characterization, and biosensing applications of DNA aptamers targeting cyanotoxin BMAA

“…The GUI of the FASTAptamerR 2.0 (ref. 45) pipeline was used for sequence counts, sequence enrichment, clustering, motif analysis across populations, data ltration, and plotting. Enrichment is dened as the normalized values (reads per million) of the last round of selection (R18) divided by the normalized values of the library control (R0).…”

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

“…We next compared the capabilities and output of AptamerRunner to the capabilities and output of FASTAptamer, FASTAptameR 2.0 and AptaCluster (22)(23)(24)34). Details and features of FASTAptamer, FASTAptameR 2.0, AptaCluster and AptamerRunner are summarized in Table 1.…”

“…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.…”