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cTFbase: a database for comparative genomics of transcription factors in cyanobacteria

Jinyu Wu1, Fangqing Zhao23*, Shengqin Wang1, Gang Deng1, Junrong Wang1, Jie Bai1, Jianxin Lu1, Jia Qu1 and Qiyu Bao1*

Author Affiliations

1 Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China

2 Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China

3 Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania 16802, USA

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BMC Genomics 2007, 8:104  doi:10.1186/1471-2164-8-104

Published: 18 April 2007

Abstract

Background

Comprehensive identification and classification of the transcription factors (TFs) in a given genome is an important aspect in understanding transcriptional regulatory networks of a specific organism. Cyanobacteria are an ancient group of gram-negative bacteria with strong variation in genome size ranging from about 1.6 to 9.1 Mb and little is known about their TF repertoires. Therefore, we constructed the cTFbase database to classify and analyze all the putative TFs in cyanobacterial genomes, followed by genome-wide comparative analysis.

Description

In the current release, cTFbase contains 1288 putative TFs identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domains and ortholog identification from any selected genomes. Comparative analysis revealed great variability of the TF sequences in cyanobacterial genomes. The high variance on the gene number and domain organization would be related to their diverse biological functions and their adaptation to various environmental conditions.

Conclusion

cTFbase provides a centralized warehouse for comparative analysis of putative TFs in cyanobacterial genomes. The availability of such an extensive database would be of great interest for the community of researchers working on TFs or transcriptional regulatory networks in cyanobacteria. cTFbase can be freely accessible at http://cegwz.com/ webcite and will be continuously updated when the newly sequenced cyanobacterial genomes are available.