NIH-led team creates aptamer binding software to tap into sequencing data boom

(By Fdardel - Own work, CC BY-SA 3.0,

Researchers at the U.S. National Institutes of Health (NIH) have led the development of software to identify sequence-structure binding motifs on aptamers. The tool is designed to support predictions about which features correspond to binding affinity and specificity, enabling researchers to cut the time it takes to identify the most promising aptamers for a particular target.

Teresa Przytycka, her colleagues at NIH and collaborators at Beckman Research Institute and Freiburg University developed the software to address a perceived gap in the aptamer discovery toolkit. Over the past few years, the declining cost of sequencing has kickstarted research into aptamers. This has led to a boom in data relating to aptamers--short RNA or DNA molecules--but, as Przytycka sees it, has also revealed a shortfall in the availability of tools capable of making use of the datasets.

AptaTRACE, the tool developed by the NIH-led team, is designed to fill this gap. Writing in the journal Cell Systems, Przytycka and her collaborators describe AptaTRACE as the first algorithm designed to use all the data generated in the current, NGS-enabled version of the systematic evolution of ligands by exponential enrichment (SELEX) protocol and identify more than one motif. And, by identifying motifs even if they are only present at low levels, the tool should accelerate the selection process.

Przytycka sees the tool as testament to the fact that the full value of datasets, however large, can only be realized with effective analysis tools. “This research is an excellent example of how the benefits of ‘big data’ critically depend upon the existence of algorithms that are capable of transforming such data into information,” Przytycka, a senior investigator at the National Center for Biotechnology Information, said in a statement.

The software, which NIH has made available to other researchers, is part of a suite of aptamer tools developed by Przytycka and her collaborators. As well as AptaTRACE, the suite includes data analysis pipeline AptaTools, experiment visualization program AptaGUI and secure database communication tool AptaREST.

- here’s the paper
- read the release