HRIBO: high-throughput analysis of bacterial ribosome profiling data
Abstract: Motivation
Ribosome profiling (Ribo-seq) is a powerful approach based on deep sequencing of cDNA libraries generated from ribosome-protected RNA fragments to explore the translatome of a cell, and is especially useful for the detection of small proteins (50–100 amino acids) that are recalcitrant to many standard biochemical and in silico approaches. While pipelines are available to analyze Ribo-seq data, none are designed explicitly for the automatic processing and analysis of data from bacteria, nor are they focused on the discovery of unannotated open reading frames (ORFs).
Results
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing and quality control steps. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary bacteria-focused tools, and integrates them with additional feature information and expression values. This facilitates the rapid and high-confidence discovery of novel ORFs and their prioritization for functional characterization
- Standort
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Deutsche Nationalbibliothek Frankfurt am Main
- Umfang
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Online-Ressource
- Sprache
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Englisch
- Anmerkungen
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Bioinformatics. - 37, 14 (2021) , 2061-2063, ISSN: 1367-4811
- Ereignis
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Veröffentlichung
- (wo)
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Freiburg
- (wer)
-
Universität
- (wann)
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2024
- Urheber
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Gelhausen, Rick
Svensson, Sarah L.
Froschauer, Kathrin
Heyl, Florian
Hadjeras, Lydia
Sharma, Cynthia M.
Eggenhofer, Florian
Backofen, Rolf
- DOI
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10.1093/bioinformatics/btaa959
- URN
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urn:nbn:de:bsz:25-freidok-2598733
- Rechteinformation
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Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Letzte Aktualisierung
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15.08.2025, 07:32 MESZ
Datenpartner
Deutsche Nationalbibliothek. Bei Fragen zum Objekt wenden Sie sich bitte an den Datenpartner.
Beteiligte
- Gelhausen, Rick
- Svensson, Sarah L.
- Froschauer, Kathrin
- Heyl, Florian
- Hadjeras, Lydia
- Sharma, Cynthia M.
- Eggenhofer, Florian
- Backofen, Rolf
- Universität
Entstanden
- 2024
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