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Ramapo College Bioinformatics Group
GRSDB - The 'G'-Rich Sequences Database

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Search Help Glossary of terms Understanding G-Scores Dealing with overlaps

Dealing with Overlapping QGRS Arrangements

Example 1: GGGTGGGGGTGATAGGATGGGGAGG
The above sequence can theoretically form 25 overlapping G-quadruplexes which may differ in total length, loop sizes and loop sequences.

Some (out of 25) potential overlapping arrangements from the above example:
  1. GGGTGGGGGTGATAGGATGGGGAGG
  2. GGGTGGGGGTGATAGGATGGGG
  3. GGGTGGGGGTGATAGG
  4.     GGGGGTGATAGGATGGGGAGG
  5.        GGTGATAGGATGGGGAGG
All of the 25 arrangements may have the potential to form intramolecular quadruplexes in the cell, many of which may be stable. In order to focus our studies on an unambiguous sequence, we have used a scoring system (1) which rewards an arrangement that is likely to form an intramolecular quadruplex. For example, out of all the possible arrangements a high scoring sequence #2 above is selected and is designated as “non-overlapping” QGRS.

 

Example 2: 9111GGGGGAGAGGACAGGGAGGAGGGATTGG 9138
Mapped near alternative splice site of the Mouse Guanylyl Cyclase-B (Npr2) gene (NCBI Accession # AH013048), the above sequence can theoretically form 16 overlapping G-quadruplexes which may differ in total length, loop sizes and loop sequences.

Some (out of 16) potential overlapping arrangements from the above example:

  1. GGGGGAGAGGACAGGGAGGAGG
  2.   GGGAGAGGACAGGGAGGAGGGATTGG
  3.         GGACAGGGAGGAGG
  4.               GGAGGAGGGATTGG
  5.   GGGAGAGGACAGGGAGGAGG

A high scoring (1) QGRS, designated as “non-overlapping” is selected (# 5 in the above example) out of all the possible arrangements

Unless specifically mentioned, all further data analysis is performed on non-overlapping QGRS.


1. D’Antonio,L. and Bagga,P.S. (2004) Computational methods for predicting intramolecular G-quadruplexes in nucleotide sequences. Computational Systems Bioinformatics, CSB 2004. Proceedings. 2004 IEEE, Pages:561-562.

Search Help Glossary of terms Understanding G-Scores Dealing with overlaps
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