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NPRD: Nucleosome Positioning Region Database
Victor G Levitsky1, Aleksey V Katokhin, Olga A Podkolodnaya
1Institute of Cytology and Genetics SB RAS, prosp. Lavrentieva 10, Novosibirsk 630090, Russia. levitsky@bionet.nsc.ru
Nucleic Acids Research
|December 21, 2004
Summary
The Nucleosome Positioning Region Database (NPRD) is the first curated resource for nucleosome formation sites (NFSs). It integrates experimental data on NFS characteristics, aiding research into gene regulation and DNA structure.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Nucleosome positioning is crucial for gene regulation.
- Experimental data on nucleosome formation sites (NFSs) are scattered.
- A centralized, curated database is needed to consolidate this information.
Purpose of the Study:
- To create the first curated database focused on nucleosome formation sites (NFSs).
- To compile and annotate experimental data on NFS locations and characteristics.
- To facilitate research on the functional and structural properties of nucleosomes.
Main Methods:
- Compilation of experimental data on NFSs from published literature.
- Detailed annotation of each NFS entry, including functional characteristics.
- Integration of data on gene activity, non-histone protein influence, and experimental methods.
Main Results:
- The Nucleosome Positioning Region Database (NPRD) is established.
- NPRD currently contains 438 entries from 124 original papers.
- The database includes detailed annotations on NFS functional characteristics and experimental parameters.
Conclusions:
- NPRD serves as a valuable resource for studying nucleosome positioning.
- The database supports research into the relationship between nucleosome structure and gene activity.
- NPRD enables advanced analysis of DNA properties and their influence on nucleosome formation.