RT Journal Article
T1 sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms.
A1 Aparicio-Puerta, Ernesto
A1 Gomez-Martin, Cristina
A1 Giannoukakos, Stavros
A1 Medina, Jose Maria
A1 Scheepbouwer, Chantal
A1 Garcia-Moreno, Adrian
A1 Carmona-Saez, Pedro
A1 Fromm, Bastian
A1 Pegtel, Michiel
A1 Keller, Andreas
A1 Marchal, Juan Antonio
A1 Hackenberg, Michael
K1 Search Engine
K1 Plants
K1 Additional Terms
AB The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.
PB Oxford University Press
YR 2022
FD 2022-04-28
LK http://hdl.handle.net/10668/19813
UL http://hdl.handle.net/10668/19813
LA en
NO Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, et al.  sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res. 2022 Jul 5;50(W1):W710-W717.
DS RISalud
RD Apr 20, 2025