Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic.

Chin-Hsien Tai, Deborah Hinton, Sung-Huan Yu

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Chin-Hsien TaiLaboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

Deborah HintonGene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

Sung-Huan YuInstitute of Precision Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan. silasysh@g-mail.nsysu.edu.tw.

Funding

Regulation of Virulence Genes in Bordetella pertussisZIADK057813 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI HINTON, DEBORAH M · 2009 to 2025

$7.7M

Intramural NIH HHS ZIA DK057813NIDDK NIH HHS INTRAMURAL PROGRAM

6 · The paper itself

Abstract

ANNOgesic is an RNA-seq analysis pipeline that can detect sRNAs and many other genomic features in bacteria and archaea. In addition to listing sRNA candidates, ANNOgesic also generates various formats of data files for visual examination and downstream experimental design. Based on validations from previous studies, the sRNA predictions are accurate and reliable. In this chapter, we outline the sRNA detection algorithm, important parameters used, step-by-step execution, and data interpretation with a B. pertussis study as an example. Following those procedures, novel sRNA can be revealed by ANNOgesic.

Indexed as

RNA, BacterialRNA, Small UntranslatedComputational BiologyGene Expression Regulation, BacterialGenome, BacterialGenomicsRNA-SeqSequence Analysis, RNARNA, BacterialRNA, Small UntranslatedANNOgesicComputational predictionsgenome annotationRNA-seqSmall RNAs

Identifiers

PMID38217648

DOI10.1007/978-1-0716-3565-0_4

PMCPMC12453237

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.