snoscan protocols

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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 in pipelines

 (4)
2013
PMCID: 3695527
PMID: 23620296
DOI: 10.1093/nar/gkt317

[…] were used for further computational analysis of the data: rna folding [mfold ()], trna gene prediction [trnascan-se (), genomic trna database ()], small nucleolar rna (snorna) gene prediction [snoscan ()], crrna identification [crisprdb ()], rna alignments [clustalw2 ()] and rna visualization [varna ()]. gene annotations were obtained from genbank., in all, 10 ng of an m. kandleri srna […]

2012
PMCID: 3542256
PMID: 22892049
DOI: 10.1186/1471-2164-13-390

[…] rrna of e. histolytica and selected five organisms was carried by emboss pair wise alignment tool separately (additional file : figure s1). this gave us putative 173 methylation and 126 psi sites., snoscan and cdseeker were used to score potential guide and orphan c/d box snornas respectively from the whole genome sequence (wgs) of e. histolytica. wgs was downloaded from ncbi […]

2012
PMCID: 3558965
PMID: 23407329
DOI: 10.4056/sigs.2645906

[…] []. annotation of transfer rna (trna) genes was established using trnascan-se [], supplemented with manual curation of non-canonical introns. c/d box srna genes were identified computationally using snoscan [] with extensions supported by transcriptional sequencing [51]. h/aca-like srna genes were identified using transcriptionally-supported homology modeling of experimentally validated srna […]

2007
PMCID: 1950533
PMID: 17586815
DOI: 10.1093/nar/gkm474

[…] not to have separate transcription start sites for snornas., the c-boxes of putative snornas are more similar to the experimentally confirmed snornas in giardia ()., all the output sequences from snoscan-g were compared against the database of giardia open-reading frames (orfs) downloaded from giardiadb (http://www.mbl.edu/giardia) to exclude possible mrna sequences. these orf datasets […]


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snoscan in publications

 (40)
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 […]

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 […]

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 […]

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., […]

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 […]


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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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