snoGPS protocols

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snoGPS specifications

Information


Unique identifier OMICS_09906
Name snoGPS
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 snoGPS 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 Peter Schattner <>

Information


Unique identifier OMICS_09906
Name snoGPS
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format FASTA, GenBank, EMBL, GCG, IG, Raw
Output data The snoGPS 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 Peter Schattner <>

Publications for snoGPS

snoGPS in pipeline

2009
PMCID: 2730528
PMID: 19763159
DOI: 10.1371/journal.pcbi.1000507

[…] human mirna encoding regions (including the mirna hairpins and 175 flanking nucleotides on either side) were scanned for the presence of box h/aca snornas using a locally-installed copy of the snogps program . in addition to known mirnas, two sets of control sequences were also scanned using snogps. the first sets of control sequences consisted of 676 randomly generated sequences […]

snoGPS in publications

 (16)
PMCID: 5033589
PMID: 27658249
DOI: 10.1371/journal.pone.0163235

[…] 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 (pseudouridylation-guide) […]

PMCID: 4696810
PMID: 26716454
DOI: 10.1371/journal.pone.0145612

[…] determined using fisher's exact test. go term enrichment analysis employed gostat using the benjamini correction method for false discovery []. small nucleolar rnas (snornas) were identified using snogps []., microarray data were as described []. array features corresponding to annotated genes were identified using blastn with a 97% identity cutoff. expression stabilities of genes […]

PMCID: 3979661
PMID: 24713982
DOI: 10.1371/journal.pone.0092946

[…] of the genus plasmodium., to identify whether the novel intergenic and intronic is-ncrnas belong to known functional classes of ncrnas, the 313 intergenic and 29 intronic is-ncrnas were analysed by snogps and snoreport . a total of 22 is-ncrnas with clear snorna characteristics were identified (). of these is-ncrnas, 20 were identified as h/aca box snorna candidates, one was identified […]

PMCID: 3890542
PMID: 24377353
DOI: 10.1186/1471-2164-14-931

[…] in archaea only), and h/aca snornas, which guide pseudouridylation in these rna species [,]., to predict the two classes of snornas and their putative targets in our data, we used the snoscan and snogps programs, defining the potential target sequences as the 5.8s, 18s, and 25s rrnas of t. rubrum and all snrnas identified in our data [,]. we identified 96 snornas, including 58c/d box snornas […]

PMCID: 3228867
PMID: 22053856
DOI: 10.1186/1471-2164-12-550

[…] constructed by rnamotif [] was tested to look for possible h/aca-like motifs in g. intestinalis contigs (figure ). results show 29 rna contigs adopted the model, and two of them overlap with the snogps-identified candidates. however, without the constraint of pre-specified target sequences, the predicted structures are not identical. interestingly, one of the h/aca-like rnas shows a possible […]

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

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