68. Interaction graphs as a way to discover multiplexes in nucleic acid structures.
Invited abstract in session FC-1: Graphs, stream Graphs.
Friday, 13:30 - 15:00Room: L226
Authors (first author is the speaker)
| 1. | Michal Zurkowski
|
| Institute of Computing Science, Poznan University of Technology | |
| 2. | Marta Szachniuk
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| Institute of Computing Science, Poznan University of Technology | |
| 3. | Tomasz Żok
|
| Institute of Computing Science, Poznan University of Technology |
Abstract
The scientific community is showing interest in nucleic acid structures containing quadruplexes and connected motifs. One of them is multiplexes which are also found together with quadruplexes. The presented algorithm will allow for the identification of those motifs and will fill another part of the knowledge that is not yet properly analyzed or gathered in databases. It will be the first method in the world dedicated to the search and identification of n-tads in nucleic acid structures. It detects quadruplex interactions with neighboring external nucleotides, which allows for the automatic identification of n-tads of any rank (tetrad, pentad, hexad) with possible future applications for a search of n-taplexes. Initial preprocessing is done with the ElTetrado tool which identifies and provides structural information about quadruplexes in the structure. Each quadruplex is analyzed individually and its nucleotides are used as starting points in the identification of the n-tads. We use their potential structural non-canonical connections as well as their geometrical 3D properties. The potential nucleotide’s slope, distance, and height differences cannot deviate too much compared to the current tetrad which the candidate would be incorporated into. All geometrical cutoff parameters were obtained from the extensive analysis of the actual structures containing those motifs.
Keywords
- Computational biology, bioinformatics and medicine
Status: accepted
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