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Software for Aptamer Sequencing Data Analyais
Software for Aptamer Sequencing Data Analyais
Software to Analyze Sequencing Data
Software to Analyze Sequencing Data
Bioinformatics: There are a number of different aptamer bioinformatic platforms. In this project, there are several that we use.
Galaxy: The goal of Galaxy is for bioinformatics tools to be more readily available to the average person with little to no programming experience. Galaxy was built for genomic data analysis but researchers have developed workflows to use Galaxy for aptamer sequencing analysis.
AptaSUITE: AptaSUITE is another platform that we explore. AptaSUITE is particularly helpful for our purposes. The program can help the user visualize and predict secondary structure.
MEME: This tool can help the researcher find common motifs.
Mfold: Mfold predicts secondary structures (Reeder et al 2006).
FASTaptamer: Amongst other things, FASTaptamer compares and ranks sequences. Generally FASTaptamer is a toolkit that is used for primary sequence analysis.
Keywords
Keywords
Bioinformatics
Bioinformatics
This involves the accumulation, storage, analysis, and spread of biological data. There are different bioinformatic tools, such as Galaxy and AptaSUITE. The goal of bioinformatics is the sharing of information amongst the scientific community.
Next Generation Sequencing (NGS)
Next Generation Sequencing (NGS)
NGS is also known as HTS or high-throughput sequencing. It is a term used to refer to many different new sequencing technologies. Next generation sequencing includes methods like Illumina sequencing. Sanger sequencing is not a part of NGS.
Data Analysis
Data Analysis
We collect data using the bioinformatic tools. Data comes in many forms. In our research, the data is the nucleotides that make up the aptamer. The data means nothing until it is analyzed. Data analysis is the inspection of data until you find useful information.
Galaxy is a program for the analysis of sequenced data and apparitions. Galaxy analyzes NGS data and lets the researcher know what is in their sample and the quality of their sample. The goal of Galaxy is to make a bioinformatic tool more accessible and user friendly (Thiel). It is important to note that no computer science background is necessary to use Galaxy.
More information can be found in the methods section.
AptaSUITE. (2018). https://drivenbyentropy.github.io
AptaSUITE
AptaSUITE
AptaSUITE is another bioinformatic tool. The purpose of AptaSUITE is to analyze data produced from high-throughput sequencing. It focuses on the storage, retrieval and manipulation of aptamers. AptaSUITE is a way to visualize what you have sequenced. It is also a way to locate patterns and motifs in your aptamer
More information can be found in the methods section
Relevant Papers
Relevant Papers
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R. Beyond Mfold: Recent advances in RNA bioinformatics. Journal of Biotechnology. 2006;124(1):41-55. doi:10.1016/j.jbiotec.2006.01.034
The first version of Mfold came about in 1981. Since then there have been many advancements in structural prediction. The paper talks about three programs that can be used to predict folding: Mfold, Sfold, and RNAsubopt. The paper focused on RNA, rather than aptamers. This field of study still has a long way to go. The paper explains how the science community seems to have learned to live with the shortcomings of secondary structure prediction. All of the services the paper talks about are available for download, and use by the public. In general, this paper was useful in learning about Mfold and the shortcomings that secondary structure prediction software still has.
Kinghorn AB, Fraser LA, Shaolin Liang, Simon Chi-Chin Shiu, Tanner JA. Aptamer Bioinformatics. International Journal of Molecular Sciences. 2017;18(12):2516. doi:10.3390/ijms18122516
This article describes the process that needs to be gone through in order to use a bioinformatic tool. They also discuss the different possible uses of bioinformatic tools. Bioinformatic tools have improved greatly in recent years. They can simulate selection and design, store data, identify common patterns, and more. It goes through the process of sequencing. The paper explains what SELEX and it goes through the steps of SELEX. The paper also discusses and explains the different methods of aptamer selection. The paper then discusses sequencing the selected aptamer.
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