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SnoReport specifications

Information


Unique identifier OMICS_06249
Name SnoReport
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SnoReport

SnoReport citations

 (24)
library_books

The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat

2018
PLoS One
PMCID: 5791967
PMID: 29385175
DOI: 10.1371/journal.pone.0189947

[…] n sites were compiled and fed into the SNOSCAN program for guide box C/D snoRNA prediction. Hits with scores higher than 20 and in the correct orientation were selected for further analysis. Both the SnoReport and SnoSeeker programs were employed to locate potential orphan box C/D snoRNAs. Output generated was compared and contrasted by using VLOOKUP function in Excel to identify similar hits gene […]

library_books

PlantRNA_Sniffer: A SVM Based Workflow to Predict Long Intergenic Non Coding RNAs in Plants

2017
Noncoding RNA
PMCID: 5831995
PMID: 29657283
DOI: 10.3390/ncrna3010011

[…] w on analyzing large datasets, CPC works well with known protein coding transcripts, but may tend to classify novel PCTs into ncRNAs, if they have not been recorded in the protein databases. PSoL [], SnoReport [], RNAsnoop [], and SnoStrip [] are methods designed to classify small ncRNAs. LncRScan-SVM [], lncRNA-MFDL [], lncRNA-ID [], lncRNApred [], PLEK [], and CNCI [] are methods that use machin […]

library_books

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification

2016
BMC Bioinformatics
PMCID: 5249026
PMID: 28105919
DOI: 10.1186/s12859-016-1345-6

[…] To verify the quality of prediction, validation on real data was performed with two experiments. In the first one, we executed snoReport 2.0 with a set of previously predicted vertebrate and invertebrate sequences, some of them partially confirmed in experiments, in humans, nematodes, drosophilids, platypus, chickens and leis […]

library_books

An updated human snoRNAome

2016
Nucleic Acids Res
PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] egions that were supported by at least five reads in the combined set of sRNA-seq samples and extended these loci by 20 nt from the 5′ end and 100 nt from the 3′ end. The predictions of snoSeeker and snoReport were pooled and candidate snoRNA genes overlapping with already annotated snoRNA genes were removed. This step yielded 820,835 putative C/D box snoRNA loci and 316,076 H/ACA box snoRNA loci. […]

library_books

The non coding RNA composition of the mitotic chromosome by 5′ tag sequencing

2016
Nucleic Acids Res
PMCID: 4889943
PMID: 27016738
DOI: 10.1093/nar/gkw195

[…] n the mCARs, we hypothesized that at least some of these novel transcripts might be previously unknown snoRNAs. We thus examined these mCARs for well-established snoRNA sequence characteristics using SnoReport and indeed identified 21 that are possibly novel C/D box snoRNA (Supplementary Table S8). Further inspection of these putatively novel snoRNA with PLEXY resulted in the identification of the […]

library_books

Promoter based identification of novel non coding RNAs reveals the presence of dicistronic snoRNA miRNA genes in Arabidopsis thaliana

2015
BMC Genomics
PMCID: 4660826
PMID: 26607788
DOI: 10.1186/s12864-015-2221-x

[…] ATAA, ATAAAT, TAAATA, ATATAT, TTATAA and TTATAT). Potential open reading frames (ORFs) of novel transcripts were predicted by ESTScan using Arabidopsis parameters []. Putative snoRNA was predicted by SnoReport (version 1.2.3) with default ‘-smart’ parameters []. RNA folding structures were predicted by RNAfold (ViennaRNA package 2) []. The Rfam database (version 12.0, http://rfam.sanger.ac.uk/) [] […]

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SnoReport institution(s)
Institute for Theoretical Chemistry, University of Vienna, Wien, Austria

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