Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium

Simple item page
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorZimmer, Ralfcs
dc.coverage.issueII.cs
dc.coverage.volume13347cs
dc.date.issued2022-06-08cs
dc.description.abstractThanks to their diversity, non-model bacteria represent an inexhaustible resource for microbial biotechnology. Their utilization is only limited by our lack of knowledge regarding the regulation of processes they are capable to perform. The problem lies in non-coding regulators, for example small RNAs, that are not so widely studied as coding genes. One possibility to overcome this hurdle is to use standard RNA-Seq data, gathered primarily to study gene expression, for the prediction of non-coding elements. Although computational tools to perform this task already exist, they require the utilization of stranded RNA-Seq data that must not be available for non-model organisms. Here, we showed that trans-encoded small RNAs can be predicted from non-stranded data with comparable sensitivity to stranded data. We used two RNA-Seq datasets of non-type strain Clostridium beijerinckii NRRL B-598, which is a promising hydrogen and butanol producer, and obtained comparable results for stranded and non-stranded datasets. Nevertheless, the non-stranded approach suffered from lower precision. Thus, the results must be interpreted with caution. In general, more benchmarking for tools performing direct prediction of small RNAs from standard RNA-Seq data is needed so these techniques could be adopted for automatic detection.en
dc.formattextcs
dc.format.extent45-56cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationLecture Notes in Computer Science. 2022, vol. 13347, issue II., p. 45-56.en
dc.identifier.doi10.1007/978-3-031-07802-6_4cs
dc.identifier.isbn978-3-031-07802-6cs
dc.identifier.issn1611-3349cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.other178441cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.scopus56309904900cs
dc.identifier.urihttp://hdl.handle.net/11012/208152
dc.language.isoencs
dc.publisherSpringer Naturecs
dc.relation.ispartofLecture Notes in Computer Sciencecs
dc.relation.urihttps://link.springer.com/chapter/10.1007/978-3-031-07802-6_4cs
dc.rights(C) Springer Naturecs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1611-3349/cs
dc.subjectSmall non-coding RNAen
dc.subjectClostridium beijerinckii NRRL B-598en
dc.subjectRNA-Seqen
dc.subjectGenome annotationen
dc.titleComparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacteriumen
dc.type.driverconferenceObjecten
dc.type.statusPeer-revieweden
dc.type.versionacceptedVersionen
sync.item.dbidVAV-178441en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:39:55en
sync.item.modts2025.01.17 16:35:07en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
9783031078026_4_accepted.pdf
Size:
858.29 KB
Format:
Adobe Portable Document Format
Description:
9783031078026_4_accepted.pdf
Download
Collections
Ústav biomedicínského inženýrství