PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots

Abstract

Pseudoknots have been recognized to be an important type of RNA secondary structures responsible for many biological functions. PseudoBase, a widely used database of pseudoknot secondary structures developed at Leiden University, contains over 250 records of pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments and sequence comparisons. To promptly address the growing analysis requests of the researchers on RNA structures and bring together information from multiple sources across the Internet to a single platform, we designed and implemented PseudoBase++, an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ (http://pseudobaseplusplus.utep.edu) maps the PseudoBase dataset into a searchable relational database including additional functionalities such as pseudoknot type. PseudoBase++ links each pseudoknot in PseudoBase to the GenBank record of the corresponding nucleotide sequence and allows scientists to automatically visualize RNA secondary structures with PseudoViewer. It also includes the capabilities of fine-grained reference searching and collecting new pseudoknot information.

Structural determinants for ligand capture by a class II preQ 1 riboswitch

“…Because an embedded hairpin in pseudoknot loops, classified as HL out type (63), is a rather unusual feature, we searched for other examples with similar topologies. The most similar example is the fluoride riboswitch (Fig.…”

A family of non-classical pseudoknots in influenza A and B viruses

“…The other loop, crossing the deep groove of the top stem, is actually significantly longer than what is required to connect the ends of the stem with 5-6 base pairs across the deep groove. Such a loop can be as small as just one nucleotide in a classical pseudoknot, 15,22 and indeed, at least 66 entries out of 309 pseudoknot structures stored in the pseudoknot database 23,24 do have such a loop. Furthermore, the nonclassical configuration of the influenza all these cases, the loop bridging the ends of two coaxially stacked stems is relatively large and contains one or more structured domains (Fig.…”

“…25,26 This SEED alignment should be considered as an update and revision of the one used in building the Rfam family (Rfam Accession RF01099) for the influenza A pseudoknot, with the addition of influenza B motif and the selection of representative pseudoknot-containing virus strains. Two representative pseudoknot sequences of influenza A and B viruses are also submitted to the pseudoknot database PseudoBase 23,24 (Accessions PKB273, PKB274).…”

Elements of RNA Secondary Structures and Their Classification

“…например, [7]); в [8] дан анализ классов псевдоузлов, введенных в различных работах по предсказанию вторичной структуры РНК по ее последовательности. В базе данных [9,10] собраны примеры псевдоузлов в экспериментально определенных структурах РНК. Однако единого способа описания элементов вторичной структуры при наличии псевдоузлов, подобного тому, который был предложен в [3][4] для описания структур, которые не содержат псевдоузлов, в настоящее время нет.…”