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TADB specifications


Unique identifier OMICS_03219
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Additional information

Publications for TADB

TADB citations


Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used to Produce Drinking Water

Genome Announc
PMCID: 5473270
PMID: 28619801
DOI: 10.1128/genomeA.00517-17
call_split See protocol

[…] contains 145 scaffolds. This draft genome sequence shows that Sph1(2015) carries genes for the production of Cpa, an adhesin commonly located at the pilus tip, as well as the tight adherence protein TadB/C. Sph1(2015) requires these proteins to initiate attachment to establish strong binding to the membrane surface. […]


Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103

Sci Rep
PMCID: 5357945
PMID: 28317865
DOI: 10.1038/srep44786

[…] lignment-free composition vector (CV) method was performed for phylogenetic analysis and the phylogenetic tree was generated using the MEGA program. The toxin-antitoxin (TA) systems were predicted by TADB. Secondary metabolite gene clusters were predicted by antiSMASH. BioVenn, a web application for the comparison and visualization of biological lists, was used for Venn diagrams drawing. […]


Global Gene Expression Analysis of Cross Protected Phenotype of Pectobacterium atrosepticum

PLoS One
PMCID: 5230779
PMID: 28081189
DOI: 10.1371/journal.pone.0169536
call_split See protocol

[…] com/, Pfam http://pfam.xfam.org/, PROSITE http://prosite.expasy.org/, ICEberg http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=467, Ecogene http://ecogene.org/, String http://string-db.org/, TADB, dndDB http://db-mml.sjtu.edu.cn/dndDB/, SMART http://smart.embl-heidelberg.de/, HAMAP http://hamap.expasy.org/, EMBL-EBI http://www.ebi.ac.uk/services, REBA […]


Global reorganisation of cis regulatory units upon lineage commitment of human embryonic stem cells

PMCID: 5407860
PMID: 28332981
DOI: 10.7554/eLife.21926.032

[…] nificant PCHi-C interactions falling inside TADs, alongside TADs reported by . To assess the strength of the TAD boundaries crossed by promoter interactions, we defined a TAD boundary strength score (TADB ∆Z score) as the difference between the smoothed directionality index values at the local maximum (end of the preceding TAD) and the local minimum (start of the following TAD). Defined this way, […]


Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu

PLoS One
PMCID: 5017713
PMID: 27611790
DOI: 10.1371/journal.pone.0162172

[…] genome sequence was completed via CRISPRfinder (http://crispr.u-psud.fr/). The putative toxin-antitoxin (TA) system, which exists in the genome sequence of Ab3, was predicted using the web-based tool TADB (http://bioinfo-mml.sjtu.edu.cn/TADB/) and RASTA-Bacteria (http://genoweb1.irisa.fr/duals/RASTA-Bacteria/). The comparative analysis of genes, including the genes involved in two-component, toxin […]


Toxin Antitoxin Systems in the Mobile Genome of Acidithiobacillus ferrooxidans

PLoS One
PMCID: 4226512
PMID: 25384039
DOI: 10.1371/journal.pone.0112226
call_split See protocol

[…] In silico screening for type II TA systems in A. ferrooxidans ATCC 23270 (NCBI RefSeq NC_011761) and ATCC 53993 (NCBI RefSeq NC_011206) was conducted using the web-based search tool TADB (http://bioinfo-mml.sjtu.edu.cn/TADB/) , an online resource of type II TA loci-relevant data from 'wet' experimental data as well as information garnered by bioinformatics analyses. We also used […]


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TADB institution(s)
State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
TADB funding source(s)
Supported by National Natural Science Foundation of China [31371261, 31670074]; Ministry of Science and Technology, China (973 program) [2015CB554202].

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