Development of an online computational platform for the analysis of protein synthesis and detection of novel translated regions

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Kiniry, Stephen J.
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University College Cork
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Ribosome profiling is a technique that allows us to capture and sequence mRNA fragments protected by ribosome complexes. Mapping these ribosome protected fragments or RPFs, back to a genome or transcriptome provides information on the precise location of elongating ribosomes. This data can then be used to detect novel translated regions, translational pausing and differentially translated genes. Chapter 2 describes the development of Trips-Viz, an interactive online platform for the exploration and visualisation of RPFs mapped to the transcriptomes of various different organisms. This allows users to rapidly aggregate and visualise ribosome profiling data at a single transcript level allowing for visual detection of translated open reading frames. Trips-Viz also allows users to rapidly assess the quality of data through various meta-information plots as well as detect and visualise transcripts that are differentially expressed/translated between two conditions. These analyses can be carried out through a GUI, meaning users do not need any prior coding or command line experience to be able to use them. Chapter 3 describes the major updates made to Trips-Viz since its original publication. This includes the addition of mass spectrometry data. Several thousand human mass spectrometry datasets have been processed and detected peptides mapped to the human transcriptome in the same manner as ribosome profiling data. This allows users to corroborate the evidence from the ribosome profiling data and provides information on whether a translated ORF is capable of producing a stable protein product. The differential expression/translation detection has also been improved with the inclusion of the Deseq2 and Anota2seq software. A method for the automatic detection of translated ORFs was also included which allows users to find translated uORFs, nested ORFs, downstream ORFs in a relatively timely manner. Other improvements include the addition of help videos to guide users through the navigation and interacting with the users interface of Trips-Viz. Finally, incorporating the relevant scripts into RiboGalaxy made it easier for users to upload their own data and transcriptomes to Trips-Viz without any requirement for command line expertise.
Ribosome profiling , Translation , Transcription , Proteomics , Bioinformatics
Kiniry, S. J. 2021. Development of an online computational platform for the analysis of protein synthesis and detection of novel translated regions. PhD Thesis, University College Cork.