Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome

Alexander Herbig, Cynthia Sharma, Kay Nieselt

Abstract


RNA deep-sequencing (RNA-seq) has been revolutionizing transcriptome analyses. Despite the high-throughput nature of this technology, very often transcriptome features such as transcription start sites (TSS) are still manually annotated. The problem is compounded for comparative transcriptomics of several species. We developed the SuperGenome algorithm, a novel general approach to comparative and integrative analysis of RNA-seq data. The SuperGenome can be utilized for comparative analyses of gene expression data, promoter sequences or SNPs in several species. Furthermore, it can be used for the comparative detection of TSS, for which we developed an automated TSS prediction method for differential RNA-seq experiments.


Keywords


next generation sequencing; transcriptome; ncRNAs; promoter sequences; bioinformatics

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DOI: http://dx.doi.org/10.14806/ej.19.A.617

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