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snoSeeker specifications

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Unique identifier OMICS_09907
Name snoSeeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

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Unique identifier OMICS_09907
Name snoSeeker
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for snoSeeker

snoSeeker citations

 (15)
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

[…] rams 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 generated by both SnoReport and SnoSeeker program. […]

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

[…] eishmania. Tables and show the summary of these results in vertebrates and invertebrates organisms, respectively. Yang et al. [] identified 54 snoRNAs, 21 C/D box and 32 H/ACA box in human, using snoSeeker, a method based on probabilistic models, pairwise whole-genome alignments of eukaryotes, in which the user can include information of the putative target region or not (to find orphan snoRNA […]

library_books

An updated human snoRNAome

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

[…] To uncover additional snoRNA genes that have supporting expression evidence, we first collected predictions of two computational tools, snoSeeker () and snoReport (), that have been specifically designed to predict snoRNA genes. Due to the high computational demand of these tools, we restricted the search space to genomic regions that […]

library_books

Functional and Structural Characterization of FAU Gene/Protein from Marine Sponge Suberites domuncula

2015
Mar Drugs
PMCID: 4515611
PMID: 26198235
DOI: 10.3390/md13074179

[…] snoSeeker was used to identify snoRNAs in introns of FAU genes []. Rfam [], snOPY (http://snoopy.med.miyazaki-u.ac.jp/) and the snoRNA-LBME databases [] were used to check whether snoRNAs match to any […]

library_books

Rapid Birth and Death Evolution of Imprinted snoRNAs in the Prader Willi Syndrome Locus: Implications for Neural Development in Euarchontoglires

2014
PLoS One
PMCID: 4063771
PMID: 24945811
DOI: 10.1371/journal.pone.0100329

[…] RNA genes along with the differentiation of the eutherian or its significance to mammalian neural development. In this study, using a genome-wide snoRNA identification program developed by our group, snoSeeker , we performed comprehensive identification and evolutionary analyses to reveal the pattern and process underlying the evolution of mammalian imprinted snoRNAs. […]

library_books

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand Specific Direct RNA Sequencing, RNA Seq and ESTs

2014
PLoS One
PMCID: 3983147
PMID: 24722185
DOI: 10.1371/journal.pone.0094270

[…] n this region (, Track G, 3). This peak does not show the two-peak structure characteristic of mature miRNA sequences (see Section 4), leaving us to speculate on the nature of this short feature. The SnoSeeker (v1.1, ) snoRNA prediction algorithm predicts a snoRNA coincident with this position suggesting that this is a previously undiscovered snoRNA gene. The details for the novel gene structure a […]


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snoSeeker institution(s)
Key Laboratory of Gene Engineering of the Ministry of Education, Zhongshan University Guangzhou, China

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