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


METHODS
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.


CONCLUSIONS
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/ and will be continuously updated when the newly sequenced cyanobacterial genomes are available.
Wu
Jinyu
J
Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China. iamwujy@yahoo.com.cn <iamwujy@yahoo.com.cn>
Zhao
Fangqing
F
Wang
Shengqin
S
Deng
Gang
G
Wang
Junrong
J
Bai
Jie
J
Lu
Jianxin
J
Qu
Jia
J
Bao
Qiyu
Q
D000465:Algorithms; D000458:Cyanobacteria / Q000235:genetics*; D030541:Databases, Genetic; D023281:Genomics; D020407:Internet; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*; D014584:User-Computer Interface
D014157:Transcription Factors