A deep learning-based method to predict bARTTs. Bioinformatics 2024, 40(7):btae378.
ADP-ribosylation is a critical post-translational modification involved in regulating diverse cellular processes. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent virulence factors that orchestrate the manipulation of host cell functions to facilitate bacterial pathogenesis. We proposed a deep learning-based model specifically engineered to predict bARTTs from bacterial genomes. |
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The database of VgrG from T6SS. Commun Biol 2023, 6(1):1195.
The VgrG protein is a central component of the spike complex of the type VI secretion system (T6SS), and it interacts with the cognate effectors with the aid of adaptors and co-effectors. Previous studies have revealed that T6SS adaptor and co-effector proteins are usually encoded between vgrG genes and the cognate effectors. Therefore, VgrG is a good marker to explore potential undiscovered adaptors and co-effectors. |
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The database of zoonotic and vector-borne viruses. Nucleic Acids Res 2022, 50(D1):D943-D949.
The majority of emerging infectious disease outbreaks are caused by zoonotic/vector-borne viruses. The ZOVER database is dedicated to providing integrated and comprehensive virological, ecological, and epidemiological data to enhance our knowledge of zoonotic and vector-borne viruses. Currently collects zoonotic viruses from two major mammalian hosts (bats and rodents) and vector-borne viruses from two main arthropod vectors (mosquitos and ticks). |
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The database of toxin complexes. PLOS Pathogens 2021, 17(2):e1009102.
The toxin complex (TC) is composed of three components: TcA, TcB and TcC. It's initially identified in Photorhabdus luminescens as an insecticidal toxin. But we identified 1,608 potential Tc loci from complete and draft genomes of both Gram- and Gram+ bacteria via a protein HMM profile and genomic context-based approach. |
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An end-to-end deep convolutional neural network model that can automatically learn expressive feature representations for classification of bacterial virulence factors. Bioinformatics 2020, 36(12):3693-3702.
VFNet is implemented in Python with Keras library and the TensorFlow backend. The source code and datasets of VFNet are available for download. |
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The database of extracellular contractile injection (eCIS) systems. Cell Reports 2019, 29(2):511-521.
The eCIS systems represent a novel class of relatively poorly characterized bacterial effector delivery devices. Known eCIS systems include AFP from Serratia entomophila, PVC from Photorhabdus luminescens and MAC from Pseudoalteromonas luteoviolacea. We further identified 631 potential eCIS loci from 11,699 complete bacterial genomes using a bioinformatic approach. |
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The database of rodent-associated viruses. J Genet Genomics 2017, 44(5):259-264.
Rodents are most abundant and diversified order of living mammals in the world, representing about 43% of the total number of mammalian species. Rodents are known reservoirs of a range of human pathogens, including hantaviruses and lassa virus. The DRodVir has been focused on exploring viral diversity in rodents. |
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The database of bat-associated viruses. Database (Oxford) 2014, 2014:bau021.
Bats are one of the most successful mammalian orders and are suggested to be important reservoir hosts of many zoonotic viruses that can cross species barriers to infect humans and other domestic or wild mammals, including lyssaviruses, henipaviruses, ebolaviruses, marburgviruses, and coronaviruses. DBatVir was therefore created to facilitate further studies by providing comprehensive, up-to-date, and well-curated information to the scientific community worldwide. |
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Trichophyton rubrum expression database. BMC Genomics 2007, 8:250.
Trichophyton is a keratinophilic filamentous fungus that infect the human hair, skin and nails. Trichophyton rubrum is the most common causative agent of dermatophytosis worldwide, such as tinea capitis, tinea corporis, tinea inguinalis, tinea manus, tinea unguim and tinea pedis. |
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An integrated database for comparative genomics of Shigella. Nucleic Acids Res 2006, 34:D398-D401.
Shigella is a group of Gram-negative, facultative intracellular pathogens that cause bacillary dysentery or shigellosis. Shigella grows only in the intestinal tract of humans. It's transmitted by the fecal-oral route. ShiBASE focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format. |
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A whole genome comparison and visulization tool. J Microbiol Meth 2003, 54:423-426.
GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains. It is a stand-alone graphical user interface (GUI) program implemented in Perl/Tk. |
