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Functional Annotation of Custom Transcriptomes

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Alternative Splicing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2537))

Abstract

Many eukaryotic genes can give rise to different alternative transcripts depending on stage of development, cell type, and physiological cues. Current transcriptome-wide sequencing technologies highlight the remarkable extent of this regulation in metazoans and allow for RNA isoforms to be profiled in increasingly small biological samples and with a growing confidence. Understanding biological functions of sample-specific transcripts is a major challenge in genomics and RNA processing fields. Here we describe simple bioinformatics workflows that facilitate this task by streamlining reference-guided annotation of novel transcripts. A key part of our protocol is the R package factR that rapidly matches custom-assembled transcripts to their likely host genes, deduces the sequence and domain structure of novel protein products, and predicts sensitivity of newly identified RNA isoforms to nonsense-mediated decay.

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Acknowledgments

This work has been supported by Biotechnology and Biological Sciences Research Council (BB/M007103/1 and BB/R001049/1), Estonian Research Council (PSG415 and PRG1095), and European Commission (H2020-MSCA-RISE-2016; Project ID 734791).

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Authors and Affiliations

  1. Centre for Developmental Neurobiology, King’s College London, London, UK

    Fursham Hamid & Eugene Makeyev

  2. Institute of Computer Science, University of Tartu, Tartu, Estonia

    Kaur Alasoo & Jaak Vilo

Authors
  1. Fursham Hamid
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  2. Kaur Alasoo
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  3. Jaak Vilo
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  4. Eugene Makeyev
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Corresponding authors

Correspondence to Fursham Hamid or Eugene Makeyev .

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Editors and Affiliations

  1. Biozentrum, University of Basel, Basel, Switzerland

    Peter Scheiffele

  2. Biozentrum, University of Basel, Basel, Switzerland

    Oriane Mauger

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Hamid, F., Alasoo, K., Vilo, J., Makeyev, E. (2022). Functional Annotation of Custom Transcriptomes. In: Scheiffele, P., Mauger, O. (eds) Alternative Splicing. Methods in Molecular Biology, vol 2537. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2521-7_9

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  • DOI: https://doi.org/10.1007/978-1-0716-2521-7_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2520-0

  • Online ISBN: 978-1-0716-2521-7

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