GUUGle specifications

Information


Unique identifier OMICS_09376
Name GUUGle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robert Giegerich <>

Information


Unique identifier OMICS_09376
Name GUUGle
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Robert Giegerich <>

Publication for GUUGle

GUUGle in publications

 (6)
PMCID: 5795987
PMID: 29295476
DOI: 10.3390/ijms19010037

[…] target prediction was performed using the tools4mirs meta-server (www.tools4mirs.org) [], with 5 different target prediction algorithms incorporated into the analysis: miranda, pita, rna22, guugle and mirmap. moreover, for each programme, restrictive parameters were set up, specifically: (1) for rna22: no g:u wobbles were allowed in the “seed” region, −19 kcal/mol was the maximum […]

PMCID: 5415748
PMID: 28468647
DOI: 10.1186/s12864-017-3725-3

[…] were then mapped to the genome of escherichia coli k12 mg1655 with blast []. only blast hits without mismatches or gaps were considered. for each read, potential helical regions were predicted using guugle []. then, chimeras (chimeric reads) were identified for subsequent analysis. here we searched for “chimeras” satisfying the following criteria: (1) read not mapped continuously to the genome; […]

PMCID: 5435917
PMID: 28334800
DOI: 10.1093/nar/gkx115

[…] efforts to design asrna have traditionally been aided by algorithms that predict rna–rna interactions (,). these approaches are numerous and stem from simple and fast surveying methods such as guugle () and blast () that score potential target regions within an rna of interest using the sole criterion of complementarity. these approaches have been followed by several methods that display […]

PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] there are also other machine learning algorithms (; ), and probabilistic approaches like ractip (), which uses the contrafold model () for rna interaction prediction., risearch (), bindigo () and guugle () are examples of alignment-like methods. the risearch algorithm was mainly developed for rapidly searching genomes to detect rna–rna pairs from genome sequencing data by combining […]

PMCID: 4838349
PMID: 26673718
DOI: 10.1093/nar/gkv1477

[…] the entire interaction complex as quantified by the overall gibbs free energy (δg) of stacking basepairs. we refer to these as ‘interaction-only’ methods, rnaduplex (), rnaplex-c (), risearch () and guugle () fall into this category. guugle is unique amongst these tools, being the only one that does not compute gibbs free energies to score optimal interactions, but instead returns all ungapped […]


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GUUGle institution(s)
Faculty of Technology, Bielefeld University, Bielefeld, Germany

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