Analyzing HT-SELEX data with the Galaxy Project tools--A web based bioinformatics platform for biomedical research.
The development of DNA and RNA aptamers for research as well as diagnostic and therapeutic applications is a rapidly growing field. In the past decade, the process of identifying aptamers has been revolutionized with the advent of high-throughput sequencing (HTS). However, bioinformatics tools that enable the average molecular biologist to analyze these large datasets and expedite the identification of candidate aptamer sequences have been lagging behind the HTS revolution. The Galaxy Project was developed in order to efficiently analyze genome, exome, and transcriptome HTS data, and we have now applied these tools to aptamer HTS data. The Galaxy Project's public webserver is an open source collection of bioinformatics tools that are powerful, flexible, dynamic, and user friendly. The online nature of the Galaxy webserver and its graphical interface allow users to analyze HTS data without compiling code or installing multiple programs. Herein we describe how tools within the Galaxy webserver can be adapted to pre-process, compile, filter and analyze aptamer HTS data from multiple rounds of selection.
Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; The François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA. Electronic address: william-thiel@uiowa.edu.
William H
WH
Thiel
Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; The François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA; The Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; The Molecular and Cell Biology Program, University of Iowa, Iowa City, IA 52242, USA. Electronic address: paloma-giangrande@uiowa.edu.
Paloma H
PH
Giangrande
D052157:Aptamers, Nucleotide / Q000235:genetics; D035843:Biomedical Research; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D052156:SELEX Aptamer Technique; D012984:Software
D052157:Aptamers, Nucleotide
Aptamer; Bioinformatics; Galaxy; High-throughput sequencing (HTS); Next-generation sequencing (NGS); SELEX