title: Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.
abstract: Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.
authors.affiliation: UTHealth Bioinformatics Service Center, ‡Center for Clinical and Translational Sciences, §School of Biomedical Informatics, ∥Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, ⊥Department of Nanomedicine and Biomedical Engineering, @School of Medicine, and #Department of Integrated Biology and Pharmacology, University of Texas Health Science Center , 6431 Fannin Street, Houston, Texas 77030, United States.
authors.forename: Emily
authors.initials: E
authors.lastname: Lu
authors.forename: Miguel-Angel
authors.initials: MA
authors.lastname: Elizondo-Riojas
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Chang
authors.forename: David E
authors.initials: DE
authors.lastname: Volk
mesh_terms: D052157:Aptamers, Nucleotide / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000639:trends; D011897:Random Allocation; D052156:SELEX Aptamer Technique / Q000379:methods* / Q000639:trends; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000639:trends; D012984:Software / Q000639:trends
chemical_list: D052157:Aptamers, Nucleotide