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PseudoBase specifications


Unique identifier OMICS_09279
Name PseudoBase
Restrictions to use None
Maintained Yes


  • person_outline F. H. D. van Batenburg

Publications for PseudoBase

PseudoBase citations


RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

PMCID: 5887150
PMID: 29437826
DOI: 10.1534/genetics.117.300567

[…] We used previously published population genomic data for D. melanogaster (), D. pseudoobscura (Pseudobase) (), Anopheles gambiae (The Anopheles gambiae ), Heliconius melpomene (), Bombyx mandarina (), Apis mellifera (), Pristionchus pacificus (), and C. briggsae () for our analyses (Table S4). […]


Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila

Genome Biol Evol
PMCID: 4943187
PMID: 27189981
DOI: 10.1093/gbe/evw116

[…] oes require a high quality multiple sequence alignment (). The calculated specificities for RNAcode using the annotated short noncoding RNA loci are high using both the UCSC alignment (0.953) and the Pseudobase alignment (0.976), so we are skeptical that the unique performance of RNAcode is due to a substantially elevated false positive rate. We speculate that these loci are unannotated, avoiding […]


Multi objective optimization for RNA design with multiple target secondary structures

BMC Bioinformatics
PMCID: 4559319
PMID: 26335276
DOI: 10.1186/s12859-015-0706-x

[…] ted RNAs are tabulated in Additional file : Tables S4 and S5.In addition to the randomly generated datasets, we constructed a two-target pseudoknot dataset based on natural RNA pseudoknots taken from Pseudobase []. The two-target ‘Pseudobase’ dataset (we call LE80 dataset) was constructed as follows: Step 1) we set i = 1; Step 2) we pick up the i-th pseudoknot from the Pseudobase dataset for singl […]


Effective alignment of RNA pseudoknot structures using partition function posterior log odds scores

BMC Bioinformatics
PMCID: 4339682
PMID: 25727492
DOI: 10.1186/s12859-015-0464-9

[…] om the PDB. The secondary structure of the 3D molecule was obtained with RNAview [], retrieved from RNA STRAND. The second dataset, denoted Dataset2, contains 36 RNA pseudoknot structures chosen from PseudoBase [,] (see Additional file : Table S2). As in the first dataset, the RNA molecules in the second dataset have a wide range of sequence lengths. The pseudoknots in these datasets can be broadl […]


Characteristics and Prediction of RNA Structure

Biomed Res Int
PMCID: 4109605
PMID: 25110687
DOI: 10.1155/2014/690340

[…] for mixed data of pseudoknot-free and pseudoknotted sequences. We select two data sets. One is TT2NE data set to test pseudoknotted structures. This data set contains 47 pseudoknotted sequences from PseudoBase and PDB. Another is PKNOTS data set to test secondary and pseudoknotted structures. This data set includes 116 sequences, including 25 tRNA sequences randomly selected from the Sprinzl tRNA […]


A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests

Evol Bioinform Online
PMCID: 3629938
PMID: 23641141
DOI: 10.4137/EBO.S10580

[…] The experimental data sets are obtained from PseudoBase and RNA SSTRAND websites. We retrieve all PseudoBase and RNA SSTRAND tRNA sequences and their secondary structure information. The sequences are then fed into pknotsRG, RNAStructure, and NU […]


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PseudoBase institution(s)
Group Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, Leiden, Netherlands; Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands

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