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Plant cis-acting regulatory DNA elements (PLACE) database: 1999

K Higo1, Y Ugawa, M Iwamoto

  • 1Department of Genetic Resources, National Institute of Agrobiological Resources, 2-1-2 Kannondai, Tsukuba,Ibaraki 305, Japan. kenhigo@abr.affrc.go.jp

Nucleic Acids Research
|December 10, 1998
PubMed
Summary

The Plant cis-Acting Regulatory DNA Elements (PLACE) database compiles plant cis-acting regulatory DNA motifs. It offers motif sequences, descriptions, and literature links, with a Signal Scan tool for sequence analysis.

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • Plant cis-acting regulatory DNA elements control gene expression.
  • Identifying these elements is crucial for understanding gene regulation in plants.
  • Existing databases may lack comprehensive or up-to-date information on these motifs.

Purpose of the Study:

  • To present the Plant cis-Acting Regulatory DNA Elements (PLACE) database.
  • To provide a centralized resource for plant cis-acting regulatory DNA motifs.
  • To offer tools for searching and analyzing these motifs in plant sequences.

Main Methods:

  • Compilation of nucleotide sequence motifs from published literature on vascular plant genes.
  • Inclusion of motif variations across different genes and plant species.

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  • Development of a web-based Signal Scan program for sequence analysis.

    • Main Results:

    • The PLACE database contains motif sequences, definitions, descriptions, and literature references (PubMed IDs, GenBank accessions).
    • The Signal Scan tool allows users to search query sequences for cis-elements.
    • Search results provide access to motif documents and linked external databases.

    Conclusions:

    • The PLACE database serves as a valuable resource for plant cis-acting regulatory DNA elements.
    • It facilitates the identification and analysis of regulatory motifs in plant genomes.
    • The integrated tools enhance the utility of the database for researchers.