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PseudoBase++ specifications


Unique identifier OMICS_09265
Name PseudoBase++
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No


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PseudoBase++ citations


Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] o this general database, there are specialized databases containing particular structural or functional classes of elements, some of which are overrepresented in viruses. The database of pseudoknots (Pseudobase++) contains 252 virus records (accessed in June 2017). IRESite contains 44 viral IRES entries (June 2017; Mokrejs et al., ). Recode contains many viral recoding sites, in particular RNA ele […]


Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

BMC Struct Biol
PMCID: 3952952
PMID: 24564983
DOI: 10.1186/1472-6807-13-S1-S3

[…] The first dataset, compiled from the RFAM database, consists of 50 non-pseudoknotted sequences and the lengths of sequences range from 127 to 568 bases. The second dataset, compiled from the RFAM and Pseudobase++ [,] databases, consists of 23 pseudoknotted sequences, and the lengths of the sequences in this dataset range from 77 to 451 bases. Note that there are no large datasets of experimentally […]

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PseudoBase++ institution(s)
Department of Computer and Information Sciences, University of Delaware, Newark, Delaware; Department of Computer Science; Bioinformatics Program; Border Biomedical Research Center, The University of Texas at El Paso, USA; Section Theoretical Biology, Leiden Institute of Biology; Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands; Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX, USA
PseudoBase++ funding source(s)
Texas Advanced Research Program (003661-0008-2006, 003661-0013-2007); the National Institutes of Health (S06GM08012-38, 5G12RR008124-11, 3T34GM008048-20S1); the National Science Foundation (DMS0800272); the CRA-W Distributed Research Experiences for Undergraduates Program 2008

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