Computational identification of plant transcription factors and the construction of the PlantTFDB database.
Methods Mol Biol
; 674: 351-68, 2010.
Article
en En
| MEDLINE
| ID: mdl-20827602
Transcription factors (TFs) play an important role in gene regulation. Computational identification and annotation of TFs at genome scale are the first step toward understanding the mechanism of gene expression and regulation. We started to construct the database of Arabidopsis TFs in 2005 and developed a pipeline for systematic identification of plant TFs from genomic and transcript sequences. In the following years, we built a database of plant TFs (PlantTFDB, http://planttfdb.cbi.pku.edu.cn ) which contains putative TFs identified from 22 species including five model organisms and 17 economically important plants with available EST sequences. To provide comprehensive information for the putative TFs, we made extensive annotation at both the family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of the TFs in other species. PlantTFDB has a simple interface to allow users to make text queries, or BLAST searches, and to download TF sequences for local analysis. We hope that PlantTFDB could provide the user community with a useful resource for studying the function and evolution of transcription factors.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Proteínas de Plantas
/
Plantas
/
Factores de Transcripción
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Biología Computacional
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Bases de Datos de Proteínas
Tipo de estudio:
Diagnostic_studies
/
Prognostic_studies
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2010
Tipo del documento:
Article
País de afiliación:
China
Pais de publicación:
Estados Unidos