Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research

Thiel, William H.; Giangrande, Paloma H.

doi:10.1016/j.ymeth.2015.10.008

Cited by 39 publications

(37 citation statements)

References 19 publications

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“…All the developed scripts can be used in galaxy cloud, [12] which can be crucial for clustering, as an elastic cloud platform properly provides the computational capacity, necessary for clustering, without installation and adjustment of the software on a local computer.…”

Section: Discussionmentioning

confidence: 99%

Untitled

Skrylnik

2017

AJP

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Aim: Implementing deep sequencing for analysis of DNA aptamer selection results requires for specialized bioinformatic software. Analysis steps include search for homologous sequences, clustering, and comparing cluster enrichment across different samples. These procedures allow deeper characterization of selected sequences by target affinity, non-specific amplification, and off-target binding, thus highlighting most promising variants or motifs. Materials and Methods: Sequencing results of systematic evolution of ligands by exponential enrichment for 40 nucleotide aptamers against extracellular CD47 protein were used as datasets for comparative clustering. Modified fast clustering script was developed based on FASTAptamer-Cluster and adapted as a galaxy tool. The algorithm was modified to terminate calculations after achieving the threshold value, and an exceeding edit distance was then assigned to non-matching pair of sequences. Results and Discussion: We have developed a set of galaxy compatible applications for rapid clustering of sequencing results and further comparative analysis of clusters. Our clustering algorithm is specifically optimized for searching for highly homologous sequences that usually form aptamer clusters and provides an average 8.4-fold increase in speed. Conclusion: Our modified clustering algorithm substantially surpasses existing alternatives in speed, thus simplifying analysis of large data sets, while its Galaxy version allows easy integration in standard workflows for preprocessing and analysis of the deep sequencing results.

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Section: Discussionmentioning

confidence: 99%

Untitled

Skrylnik

2017

AJP

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“…For downstream data analysis, please refer to “Analyzing HT-SELEX data with the Galaxy Project tools – A web based bioinformatics platform for biomedical research” [41] and http://www.medicine.uiowa.edu/humangenetics/genomics/.…”

Section: Methodsmentioning

confidence: 99%

In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs

Urak

Shore

Rockey

et al. 2016

Methods

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Aptamers are single-stranded DNA or RNA oligonucleotides that can bind with exquisitely high affinity and specificity to target molecules and are thus often referred to as ‘nucleic acid’ antibodies. Oligonucleotide aptamers are derived through a process of directed chemical evolution called SELEX (Systematic Evolution of Ligands by Exponential enrichment). This chemical equivalent of Darwinian evolution was first described in 1990 by Tuerk & Gold and Ellington & Szostak and has since yielded aptamers for a wide-range of applications, including biosensor technologies, in vitro diagnostics, biomarker discovery, and therapeutics. Since the inception of the original SELEX method, numerous modifications to the protocol have been described to fit the choice of target, specific conditions or applications. Technologies such as high-throughput sequencing methods and microfluidics have also been adapted for SELEX. In this chapter, we outline key steps in the SELEX process for enabling the rapid identification of RNA aptamers for in vivo applications. Specifically, we provide a detailed protocol for the selection of chemically-optimized RNA aptamers using the original in vitro SELEX methodology. In addition, methods for performing next-generation sequencing of the RNAs from each round of selection, based on Illumina sequencing technology, are discussed.

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“…Web-based and offline preprocessing software, such as Galaxy [54], cutadapt [55] and AptaTools [56] are often used to first isolate variable aptamer regions of a defined length by removing adapter and constant region sequences. Further programs are then employed to filter this data in order to narrow down aptamer candidates for subsequent experimental testing.…”

Section: Commercially Available Ngs Platforms Previously Used For Aptmentioning

confidence: 99%