QGRS Mapper

The QGRS Mapper is a user-friendly web-based server that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. It is useful for investigating the functional relevance of the G-quadruplex structure, particularly its role in regulating gene expression by alternative processing. QGRS Mapper features an interactive graphical representation of the data, allowing the user to simultaneously visualize QGRS distribution patterns among all the alternative RNA products of a gene on a single screen.

The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. Computational approaches to study G-quadruplexes allow detailed analysis of mammalian genomes. However, there are no known, easily accessible, user-friendly tools that can compute G-quadruplexes in the nucleotide sequences. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulating polyadenylation and splicing events in mammalian transcripts. Whether quadruplex structure directly plays a role in regulating RNA processing requires investigation.

QGRS Mapper can perform analysis of the user-provided genomic sequences, e.g., promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. This feature is very useful for investigating the functional relevance of the G-quadruplex structure, particularly its role in regulating gene expression by alternative processing. In addition to providing data on the composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, QGRS Mapper features an interactive graphical representation of the data. The user can also use the graphics module to visualize QGRS distribution patterns among a gene's alternative RNA products simultaneously on a single screen.