HTSAptamotif - Identification and Analysis of Aptamer Families using HT-SELEX Data

Friday, November 08, 2013 — Poster Session IV
2:00 p.m. – 4:00 p.m.	FAES Academic Center (Upper-Level Terrace)	NLM	COMPBIO-6

Authors

J. Hoinka
A. Berezhnoy
Z.E. Sauna
E. Gilboa
T.M. Przytycka

Abstract

HT-SELEX (High Throughput SELEX) extends the classical SELEX procedure by Tuerk and Gold by including Next-Generation sequencing of the aptamer pools after each round of selection. By generating extensive sets of aptamers this methods allows for a better understanding of their properties such as binding motifs and putative target affinities. However, to fully utilize its potential, dedicated computational methods are required. In particular the ability of efficiently grouping tenth of millions of aptamers into corresponding sequence and structure families is crucial. This constitutes a non-trivial task that cannot be approached naively due to the huge number of distinct sequences, especially during early selection cycles. Here, we present HTSAptamotif, a computational tool that solves this challenge. We applied our method to a number of experimental datasets. Our findings suggest that, in contrast to common belief, functional aptamers are less likely to correspond to single, highly enriched sequences but that families of species (i.e. clusters) provide a superior predictor for the selection of possible target aptamers. In addition, our software automatically traces the identified aptamer families across selection cycles providing a high resolution insight into the poorly understood evolutionary processes governing the selection process.