snoSeeker specifications

Information


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

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Information


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 in publications

 (12)
PMCID: 5791967
PMID: 29385175
DOI: 10.1371/journal.pone.0189947

[…] 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 generated […]

PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] data did not sufficiently or completely cover the loci., 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 […]

PMCID: 4515611
PMID: 26198235
DOI: 10.3390/md13074179

[…] the amplified fragments were separated on a 0.8% agarose gel, purified and cloned into the pgem-t vector (promega, madison, wi, usa). positive clones were sequenced using t7/puc primers., 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 […]

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

[…] 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 […]

PMCID: 3861888
PMID: 24396270
DOI: 10.2174/13892029113149990005

[…] using deep sequencing technologies to detect mirnas, other small ncrna molecules such as snorna, pirna, endo-sirna, are also identified by deep sequencing technologies. for example, we can apply snoseeker which can identify snornas from deep sequencing data []. (table ) lists the main software tools for the ncrna discovery., indeed, the main disadvantage of the popular software tools […]


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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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