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Citations per year

Number of citations per year for the bioinformatics software tool GUUGle
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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

Versioning


No version available

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 citations

 (6)
library_books

Detection of Plant miRNAs Abundance in Human Breast Milk

2017
Int J Mol Sci
PMCID: 5795987
PMID: 29295476
DOI: 10.3390/ijms19010037

[…] therefore 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 folding […]

library_books

Detecting RNA RNA interactions in E. coli using a modified CLASH method

2017
BMC Genomics
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; ( […]

library_books

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

2017
Nucleic Acids Res
PMCID: 5435917
PMID: 28334800
DOI: 10.1093/nar/gkx115

[…] tional 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 va […]

library_books

A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

2016
Bioinformatics
PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] gion. 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 the Smith-W […]

library_books

A comprehensive comparison of general RNA–RNA interaction prediction methods

2015
Nucleic Acids Res
PMCID: 4838349
PMID: 26673718
DOI: 10.1093/nar/gkv1477

[…] and fourth spot. Surprisingly, IntaRNA has minimal change to the number of predicted basepairs even with the suboptimal, meaning that the validated interactions are often its MFE prediction already. GUUGle, which simply returns all valid ungapped interactions, does surprisingly well with an MCC of 0.44 if we simply take all predictions greater than 9 basepairs (mean 9.90). It obtains a TPR equal […]

library_books

An assessment of bacterial small RNA target prediction programs

2015
RNA Biol
PMCID: 4615726
PMID: 25760244
DOI: 10.1080/15476286.2015.1020269

[…] e identification of RNA-RNA interactions can be grouped in 3 main categories that we term “alignment-like,” “inter-RNA” and “independent fold.” The “alignment-like” category includes programs such as Guugle and RIsearch that can quickly scan large sequence files for reverse complements of a given RNA sequence. While Guugle looks only for stretches of Watson-Crick or G:U matches, RIsearch implement […]


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

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