GRSDB: G-Rich Sequences DataBase
GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. Computations were performed with the help of an indigenously developed and previously published software program QGRS Mapper.
What is new in GRSDB2: The entire database has been built with a new and much improved version of QGRS Mapper program. It contains data from a large number of eukaryotic genes from several organisms in addition to human and mouse. The data model is different than the first version in that it is centered around Entrez Gene rather than solely GenBank/RefSeq nucleotide entries. The search module has been greatly enhanced. It is possible to search the database with Entrez Gene ID, Gene Name, Gene Symbols, Aliases, relevant Accession numbers and many other parameters like numbers of poly A signals and alternatively spliced products. Complex queries can also be performed. In addition, it is now possible to search the database with Gene Ontology terms. The list of genes matching the query can be sorted. The website also allows to manipulate the list to form sets of genes and perform further computations on these sets through a 'Workbench'.
The Gene View, Data View and Graphic View for individual datanbase entries have been significantly enhanced with several additional computational capabilities and links. The data can now be exported into Excel for further analysis. In addition, we have added a Sequence View which displays mapped G-quadruplexes in the context of pre-mRNA sequence.
Kikin, O., Zappala, Z., D'Antonio, L., and Bagga, P. (2008) GRSDB2 and GRS_UTRdb: Databases of Quadruplex Forming G-rich Sequences in pre-mRNAs and mRNAs. Nucleic Acids Res. 36(suppl_1): p. D141-D148