piwik-script

Intern
    Institut für Virologie und Immunbiologie

    PRICE

    PRICE (Probabilistic inference of codon activities by an EM algorithm) is a method to identify ORFs using Ribo-seq experiments embedded in a pipeline for data analysis

    Project wiki: https://github.com/erhard-lab/gedi/wiki/Price

    Software download: https://github.com/erhard-lab/gedi/releases

    GRAND-SLAM

    Globally refined analysis of newly transcribed RNA and decay rates using SLAM-seq (GRAND-SLAM) is a computational approach to infer the proportion and the corresponding posterior distribution of new and old RNA for each gene from SLAM-seq experiments.

    Project wiki: https://github.com/erhard-lab/gedi/wiki/GRAND-SLAM

    Software download: Please inquiry at Florian.Erhard at uni-wuerzburg.de

    HSV-1 Viewer

    Since the genome of herpes simplex virus 1 (HSV-1) was first sequenced more than 30 years ago, its predicted 80 genes have been intensively studied. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identified a total of 201 viral transcripts and 284 open reading frames (ORFs) including all known and 46 novel large ORFs. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of novel viral ORFs as well as N-terminal extensions (NTEs) and truncations thereof. We show that key viral regulators and structural proteins possess NTEs, which initiate from non-canonical start codons and govern subcellular protein localization and packaging. We validated a novel non-canonical large spliced ORF in the ICP0 locus and identified a 93 aa ORF overlapping ICP34.5 that is thus also deleted in the FDA-approved oncolytic virus Imlygic. Finally, we extend the current nomenclature to include all novel viral gene products.

    To make the annotation and all the obtained data readily accessible to the research community, we here provide our HSV-1 genome browser software. Thereby, viral gene expression and all data can be visually examined from whole genome to single-nucleotide resolution.

    Download at zenodo

    Hinweis zum Datenschutz

    Mit 'OK' verlassen Sie die Seiten der Universität Würzburg und werden zu Facebook weitergeleitet. Informationen zu den dort erfassten Daten und deren Verarbeitung finden Sie in deren Datenschutzerklärung.

    Hinweis zum Datenschutz

    Mit 'OK' verlassen Sie die Seiten der Universität Würzburg und werden zu Twitter weitergeleitet. Informationen zu den dort erfassten Daten und deren Verarbeitung finden Sie in deren Datenschutzerklärung.

    Kontakt

    Institut für Virologie und Immunbiologie
    Versbacher Straße 7
    97078 Würzburg

    E-Mail

    Suche Ansprechpartner

    Medizin, Geb. E5
    Medizin, Geb. E5