title: QuadBase2: web server for multiplexed guanine quadruplex mining and visualization.
abstract: DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way.
authors.affiliation: GNR Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110 025, India.
authors.forename: Parashar
authors.initials: P
authors.lastname: Dhapola
authors.affiliation: GNR Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110 025, India Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110 025, India shantanuc@igib.res.in.
authors.forename: Shantanu
authors.initials: S
authors.lastname: Chowdhury
mesh_terms: D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics; D054856:G-Quadruplexes; D016678:Genome; D055106:Genome-Wide Association Study; D006147:Guanine / Q000737:chemistry; D016247:Information Storage and Retrieval; D020407:Internet; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D011387:Prokaryotic Cells / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D006147:Guanine