
QGRS Mapper Help: Glossary
Term 
Definition 
GGroup 
The set of G's that form a tetrad, the foundation for the Gquadruplex structure. There are four such groups in a quadruplex. Each group will be of the same size in a particular quadruplex, and in any case must contain at least two G's. 
Each QGRS is assigned a score based on a system which rewards an arrangement of 'G's that is likely to form a unimolecular quadruplex. For calculation of Gscores, the size and distribution of the gaps in the predicted QGRS is taken into consideration. Also, the larger the size of the Ggroups, the higher the score. The computed Gscores are dependent on the user selected maximum QGRS length. The highest possible Gscore, using the default maximum QGRS length of 30, is 105. 

Gap or Loop 
The part of a QGRS that lies between two Ggroups. For example, in the QGRS, (GG)GTA(GG)C(GG)TGA(GG), the four Ggroups are in parentheses, so the three gaps are GTA, C, TGA. Note: up to one gap may be of length zero. 
GRS 
General term for a GRich Sequence. 
GQuadruplex 
A three dimensional structure consisting of tetrads of G's connected by Hoogsteen bonds. Each tetrad is formed by taking one G from each Ggroup. The size of the Ggroup determines the number of tetrads found in the quadruplex. 
QGRS 
GRS that have the potential to form GQuadruplex. The pattern for a QGRS is four groups of G's connected by arbitrary bases between each group. 
Near RNA Processing Sites 
A QGRS is defined to be near an RNA processing sites if it's starting position is within 120 nucleotides of the site. Exception: This distance is 200 nt upstream or downstream of a polyA signal 
Nonoverlapping QGRS 
Two sequences are said to be nonoverlapping if their positions in the nucleotide sequence do not overlap. The default action of QGRS Mapper is to only display nonoverlapping sequences (although the user can show all sequences if they choose). 
Overlapping QGRS 
Two QGRS are said to overlap if their positions in the nucleotide sequence overlap. Overlaps are eliminated by selecting for higher scoring sequence. 


Visitors 