Term

Definition

G-Group

The set of G's that form a tetrad, the foundation for the G-quadruplex 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.

G-Score

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 G-scores, the size and distribution of the gaps in the predicted QGRS is taken into consideration. Also, the larger the size of the G-groups, the higher the score. The computed G-scores are dependent on the user selected maximum QGRS length. The highest possible G-score, using the default maximum QGRS length of 30, is 105.

Gap or Loop

The part of a QGRS that lies between two G-groups. For example, in the QGRS, (GG)GTA(GG)C(GG)TGA(GG), the four G-groups 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 G-Rich Sequence.

G-Quadruplex

A three dimensional structure consisting of tetrads of G's connected by Hoogsteen bonds. Each tetrad is formed by taking one G from each G-group. The size of the G-group determines the number of tetrads found in the quadruplex.

QGRS

GRS that have the potential to form G-Quadruplex. 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

Non-overlapping QGRS

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.