Detail publikace

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

SEDLÁŘ, K. ZIMMER, R.

Originální název

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

Typ

článek ve sborníku ve WoS nebo Scopus

Jazyk

angličtina

Originální abstrakt

Thanks 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.

Klíčová slova

Small non-coding RNA; Clostridium beijerinckii NRRL B-598; RNA-Seq; Genome annotation

Autoři

SEDLÁŘ, K.; ZIMMER, R.

Vydáno

8. 6. 2022

Nakladatel

Springer Nature

ISBN

978-3-031-07802-6

Kniha

Lecture Notes in Bioinformatics

Edice

13347

Číslo edice

II.

ISSN

1611-3349

Periodikum

Lecture Notes in Computer Science

Ročník

13347

Číslo

II.

Stát

Italská republika

Strany od

45

Strany do

56

Strany počet

12

URL

https://link.springer.com/chapter/10.1007/978-3-031-07802-6_4

Plný text v Digitální knihovně

http://hdl.handle.net/11012/208152

BibTex

@inproceedings{BUT178441,
  author="Karel {Sedlář} and Ralf {Zimmer}",
  title="Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium",
  booktitle="Lecture Notes in Bioinformatics",
  year="2022",
  series="13347",
  journal="Lecture Notes in Computer Science",
  volume="13347",
  number="II.",
  pages="45--56",
  publisher="Springer Nature",
  doi="10.1007/978-3-031-07802-6\{_}4",
  isbn="978-3-031-07802-6",
  issn="1611-3349",
  url="https://link.springer.com/chapter/10.1007/978-3-031-07802-6_4"
}

Dokumenty

manuscript.pdf