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snoscan specifications

Information


Unique identifier OMICS_09905
Name snoscan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence
Input format FASTA, GenBank, EMBL, GCG, IG, Raw
Output data The snoscan outputs consist of a summary information line for each predicted snoRNA sequence, followed by the candidate.
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Todd M. Lowe

Information


Unique identifier OMICS_09905
Name snoscan
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format FASTA, GenBank, EMBL, GCG, IG, Raw
Output data The snoscan outputs consist of a summary information line for each predicted snoRNA sequence, followed by the candidate.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Todd M. Lowe

Publications for snoscan

snoscan citations

 (41)
library_books

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

2018
Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] cdna (40,188/48,510) mapped to a predicted gene locus thus spanning 78% of the annotated genes (12,395/15,839). in addition, a total of 4,213 non-coding sequences were predicted using infernal, snoscan and trnascan-se. finally, repetitive elements were annotated using repeatmasker and a species-specific library created using the repeatmodeler module. ninteen percent of the genome […]

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

[…] and signal peptides., intergenic and intronic sequences were extracted from the assembled scaffolds using the artemis genome browser [https://www.sanger.ac.uk/resources/software/artemis/] []. the snoscan program was utilized to search for guide box c/d snornas candidates targeting putative rrna methylation sites. g. antarctica ribosomal rna sequences and their methylation sites were compiled […]

library_books

First de novo draft genome sequence of Oryza coarctata, the only halophytic species in the genus Oryza

2017
F1000Res
PMCID: 5657017
PMID: 29123646
DOI: 10.5256/f1000research.13443.r26360

[…] database were also performed by using blast2go. non-coding rnas, such as mirna, trna, rrna, snorna, snrna, were identified by adopting infernal v1.1.2 ( ) using rfam database (release 9.1) ( ) and snoscan distribution. transfer rna was predicted using trnascan-se v 1.23 ( ), the o. coarctata genome (2n=4x=48; kkll; ) is self-pollinated, ( ) tetraploid plant with a genome size estimated by flow […]

library_books

Genome assembly with in vitro proximity ligation data and whole genome triplication in lettuce

2017
Nat Commun
PMCID: 5394340
PMID: 28401891
DOI: 10.1038/ncomms14953

[…] a set of custom repeat libraries as reference. additionally, trf was used to find tandem repeats., prediction of ncrna was done by type, and first trnascan-se was used to predict trnas. similarly snoscan and rnammer were used to predict snorna and rrna, respectively. infernal was used for prediction of more ncrna using the rfam database as input for mirna, rrna, rybozimes, snrna and trna., […]

library_books

Identification of Non Coding RNAs in the Candida parapsilosis Species Group

2016
PLoS One
PMCID: 5033589
PMID: 27658249
DOI: 10.1371/journal.pone.0163235

[…] and s. cerevisiae, and by similarity to ncbi blast databases. 64 ncrnas were identified in c. parapsilosis using this method., we next modified our approach by using the pattern-scanning programs snoscan and snogps to specifically identify c/d box and h/aca box snornas, respectively [, ]. snoscan predicted 24 c/d box (methylation-guide) snornas and snogps predicted 9 h/aca box […]

library_books

High throughput single base resolution mapping of RNA 2΄ O methylated residues

2016
Nucleic Acids Res
PMCID: 5388417
PMID: 28180324
DOI: 10.1093/nar/gkw810

[…] was performed using custom scripts., to identify putative snornas targeting the discovered sites, a sequence of 20 nucleotides centered on the discovered site was extracted, and passed to the snoscan software () (http://lowelab.ucsc.edu/snoscan/), with default parameters. snorna sequences were obtained from the latest ensembl release, and from deepbase predictions […]


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snoscan institution(s)
Department of Biomolecular Engineering and the UCSC RNA Center, University of California Santa Cruz, Santa Cruz, CA, USA

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