AptaSUITE

AptaSUITE Software to Interpret Sequencing Data

This page is about AptaSUITE, which is used in our project to identify aptamer candidates in the sequencing data.

AptaSUITE

AptaSUITE is a bioinformatics software used to analyze sequencing data collected from high throughput sequencing¹. The AptaSUITE software contains many features, though the main process includes: pre-processing, clustering, mutational analysis, structural analysis, and exportation. The DNA strands are pre-processed, being stripped of preparation materials such as attached bar-codes, leaving only the random region which is important for binding strength, and they are then clustered together according to similarities in sequence. We then look for for any mutations as well as structural similarities (motifs) that may increase the aptamer's binding affinity to the target molecule. The sequences and motifs which are enriched throughout selection could be key identifiers of a strong aptamer candidate. The resulting data can then be compiled into readable figures and visualizations and extracted into file format.

In our project, AptaSUITE is one software used to analyze the data collected from Illumina sequencing and outlines the key features which identify any potentially strong aptamer candidates.

Overview

AptaSUITE utilizes many different tools as part of its analyzation. This figure shows the different analyzation tools part of AptaSUITE. This includes, AptaCLUSTER, AptaTRACE, and AptaPLEX, (as outlined below), as well as AptaMUT, which is used to identify sequence mutations. The programs within AptaSUITE are used cooperatively to identify key features of an aptamer candidate capable of binding to our target molecule.

AptaSUITE Algorithms

AptaCLUSTER

An algorithm used to cluster together DNA strands according to similarities in patterns of sequences. This can show relation between sequences from different rounds of selection.

AptaTRACE

An algorithm designed to identify structural motifs in the DNA sequences and their levels of enrichment across the rounds of selection. The motifs, when present on the aptamer strand, may increase the strand's binding strength to the target molecule.

AptaPLEX

An algorithm used for initial pre-processing, as well as sorting aptamer sequencing data to match the high throughput selection rounds. AptaPLEX removes unimportant parts of the aptamer strands such as barcodes and other reagents used as part of sequencing.

Interpreting Data

AptaSUITE. (2018). https://drivenbyentropy.github.io

AptaSUITE contains many tools, including the ones described above, which all help to interpret the sequencing data. When interpreting the data, one can observe many beneficial features such as structural motifs, favorable mutations, and high levels of enrichment found on the aptamer candidates, which potentially increase the binding strength to the target molecule.

As shown in this image, one tool within AptaSUITE lists all DNA sequences within the aptamer pool, showing features such as abundance and enrichment. The data can be gathered into visualizations such as graphs (as seen on the right of the image), allowing for better organization and presentation of the sequencing data.

Relevant Sources

AptaSUITE Software Manual

Hoinka, J., Backofen, R., Przytycka, T. (2018). AptaSUITE. https://github.com/drivenbyentropy/aptasuite/wiki#aptasuite

This website contains the manual for AptaSUITE software. The manual is split into different sections, such as introductory steps on how to import sequencing data, clustering, motif analysis, and exportation of the data. It also provides some background on what is needed to run the software, including system requirements and frequent issues.

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Klingler, C., Ashley, J., Shi, K., et al. (2020). DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. FASEB Journal. 34, 4573–4590. Doi: 10.1096/fj.201902696

This study by Klingler, et al. (2020) develops aptamers against the DUX4 protein associated with FSHD (fascio-scapulo-humeral muscular distrophy, and analyzes the results using AptaSUITE. The study uses SELEX for aptamer selection for aptamer sequences targeting the DUX4 protein. The results of SELEX are then sequenced using Illumina sequencing and the data is analyzed using AptaSUITE. The results found two motifs that increased the aptamer’s binding affinity to the target DUX4 protein. The authors use AptaSUITE software to analyze data and use various data such as “cluster size” to generate figures. This relates to our method as it shows a direct application of our method, AptaSUITE, being used to analyze the results of Illumina sequencing.

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