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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 g...

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Autores principales: Wu, Jinyu, Zhao, Fangqing, Wang, Shengqin, Deng, Gang, Wang, Junrong, Bai, Jie, Lu, Jianxin, Qu, Jia, Bao, Qiyu
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858693/
https://www.ncbi.nlm.nih.gov/pubmed/17439663
http://dx.doi.org/10.1186/1471-2164-8-104
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author Wu, Jinyu
Zhao, Fangqing
Wang, Shengqin
Deng, Gang
Wang, Junrong
Bai, Jie
Lu, Jianxin
Qu, Jia
Bao, Qiyu
author_facet Wu, Jinyu
Zhao, Fangqing
Wang, Shengqin
Deng, Gang
Wang, Junrong
Bai, Jie
Lu, Jianxin
Qu, Jia
Bao, Qiyu
author_sort Wu, Jinyu
collection PubMed
description 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 and will be continuously updated when the newly sequenced cyanobacterial genomes are available.
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spelling pubmed-18586932007-04-28 cTFbase: a database for comparative genomics of transcription factors in cyanobacteria Wu, Jinyu Zhao, Fangqing Wang, Shengqin Deng, Gang Wang, Junrong Bai, Jie Lu, Jianxin Qu, Jia Bao, Qiyu BMC Genomics Database 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 and will be continuously updated when the newly sequenced cyanobacterial genomes are available. BioMed Central 2007-04-18 /pmc/articles/PMC1858693/ /pubmed/17439663 http://dx.doi.org/10.1186/1471-2164-8-104 Text en Copyright © 2007 Wu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Wu, Jinyu
Zhao, Fangqing
Wang, Shengqin
Deng, Gang
Wang, Junrong
Bai, Jie
Lu, Jianxin
Qu, Jia
Bao, Qiyu
cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title_full cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title_fullStr cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title_full_unstemmed cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title_short cTFbase: a database for comparative genomics of transcription factors in cyanobacteria
title_sort ctfbase: a database for comparative genomics of transcription factors in cyanobacteria
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858693/
https://www.ncbi.nlm.nih.gov/pubmed/17439663
http://dx.doi.org/10.1186/1471-2164-8-104
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