Khalid K. Alam, Jonathan L. Chang & Donald H. Burke "FASTAptamer: A Bioinformatic Toolkit for High-Throughput Sequence Analysis of Combinatorial Selections." Molecular Therapy — Nucleic Acids. 2015. 4, e230; DOI: 10.1038/mtna.2015.4
FASTAptamer is an easy-to-use and universally compatible toolkit designed for bench scientists to address the primary sequence analysis needs from high-throughput sequencing of combinatorial selection populations. FASTAptamer performs the simple tasks of counting, normalizing, ranking and sorting the abundance of each unique sequence in a population, comparing sequence distributions for two populations, clustering sequences into sequence families based on Levenshtein edit distance, calculating fold-enrichment for all of the sequences present across populations, and searching degenerately for nucleotide sequence motifs. While FASTAptamer was originally developed for analysis of high-throughput sequencing data from aptamer selections, it offers broad utility for those working on ribozyme or DNAzyme selections, surface display (phage display, mRNA display, etc.) selections, in vivo SELEX, protein mutagenesis selection, or any biocombinatorial selection that results in a DNA-encoded library for sequencing.