Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://bioinformatics.zj.cn/archaeatf
Full name:
Description: The ArchaeaTF is a collection of putative transcription factors (TFs) in the completed Archaeal genomes and contains detailed annotation information about TFs: such as basic sequence characteristics, domain architectures and sequence similarities against the linked databases. Moreover, ArchaeaTF can serve as a useful platform for comparative genomics analysis of TFs in Archaea, which may helps users to analyze, utilize and understand the data more effectively.
Year founded: 2007
Last update: 2008
Version: 2.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Wenzhou Medical College
Address:
City: Wenzhou
Province/State: Zhejiang
Country/Region: China
Contact name (PI/Team): Shengqin Wang
Contact email (PI/Helpdesk): wsqqqw@gmail.com

Publications

18035520
ArchaeaTF: an integrated database of putative transcription factors in Archaea. [PMID: 18035520]
Wu J, Wang S, Bai J, Shi L, Li D, Xu Z, Niu Y, Lu J, Bao Q.

Identification of all the transcription factors (TFs) encoded in a given genome is a prerequisite for understanding transcriptional regulatory networks. Archaea are prokaryotes that constitute one of the three main branches of organisms with an astounding diversity of habitats. In this report, we establish the ArchaeaTF database to provide an integrated information resource about TFs in Archaea, such as basic characteristics, domain architectures, and sequence similarities against the linked databases. Through its Web interface, ArchaeaTF provides three different ways for users to retrieve the data: simple browse, keyword search, and BLAST search. Moreover, ArchaeaTF can serve as a useful platform for comparative genomics analysis of archaeal TFs since it implements a series of tools, including MUSCLE for multiple sequence alignments of the DNA-binding domains, QuickTree for phylogenetic tree construction, and OrthoMCL for ortholog identification. The released ArchaeaTF 1.0 contains 2135 putative TFs from 37 completed archaeal genomes. In conclusion, we believe that ArchaeaTF will be a useful resource and convenient platform for researchers working on TFs and transcriptional regulatory networks to retrieve information from TFs in Archaea rapidly. ArchaeaTF is accessible at http://bioinformatics.zj.cn/archaeatf.

Genomics. 2008:91(1) | 17 Citations (from Europe PMC, 2021-11-27)

Ranking

All databases:
3442/5114 (32.714%)
Structure:
455/702 (35.328%)
3442
Total Rank
17
Citations
1.308
z-index

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Record metadata

Created on: 2018-01-26
Curated by:
Mengyu Pan [2018-09-21]
Mengyu Pan [2018-02-22]
Pei Wang [2018-01-26]