sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
Metadatos
Mostrar el registro completo del ítemAutor
Aparicio Puerta, Ernesto; Giannoukakos, Stavros Panagiotis; Medina Casaubón, José María; García Moreno, Adrián; Carmona Sáez, Pedro; Marchal Corrales, Juan Antonio; Hackenberg, MichaelEditorial
Oxford University Press
Fecha
2022-05-12Referencia bibliográfica
Ernesto Aparicio-Puerta... [et al.]. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms, Nucleic Acids Research, 2022;, gkac363, [https://doi.org/10.1093/nar/gkac363]
Patrocinador
European Commission 765492; Spanish Government; European Commission AGL2017-88702-C2-2-R; Chair 'Doctors Galera-Requena in cancer stem cell research'; Stichting Cancer Center Amsterdam CCA2021-9-77; Tromsoforskningsstiftelse (TFS) ['MIRevolution'] 20 SG BF; TKI-Health Holland ['AQrate' project]Resumen
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 performsmapping
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/.