- What is SilkPathDB ?
Silkworm Pathogen Database (SilkPathDB) is a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional annotation of genes and gene products, but also extensive biological information for gene expression data and corresponding researches. SilkPathDB will be help with researches on pathogens of silkworm as well as other Lepidoptera insects.
- SilkPathDB pathogens and data sources
- Virus, including nucleopolyhedrovirus infecting Bombyx mori (BmNPV), Bombyx mandarina (BomaNPV) and other Lepidoptera, Bombyx mori cypovirus (BmCPV) and Bombyx mori densovirus (BmDNV).
- Bacteria, including Bacillus bombysepticus and Bacillus thuringiensis.
- Fungi, including Beauveria bassiana, Metarhizium anisopliae and Cordyceps militaris CM01.
- Microsporidia, including Nosema bombycis CQ1, Nosema antheraeae YN, Nosema sp. PM-1, Vairimorpha necatrix BM, Nosema sp. YNPr and microspridia infecting other animals.
SilkPathDB Data Sources:
- Most genome datasets of silkworm pathogens were collected from NCBI Genome Resource.
- Genomes of microsporidian Nosema bombycis CQ1, Vairimorpha necatrix BM, Nosema antheraeae YY and Nosema sp. YNPr, and virus Bombyx mori nucleopolyhedrovirus CQ1 and Antheraea pernyi nucleopolyhedrovirus H were sequenced by SKLSGB.
- Genome data of microsporidian Nosema sp. PM-1 was kindly gifted by Prof. Wen Wang at KIZ.
All genomic data was analyzed and formated before being deposited into SilkPathDB.
- How to download SilkPathDB datasets ?
All datasets on SilkPathDB can be directly downloaded via the Download Datasets.
- How to use SilkPathDB ?
SilkPathDB provides many built-in tools for searching data and conducting analysis.
- Search SilkPathDB data
All genome data of silkworm pathogens can be searched by the SilkPathDB Data Search tool on top of the website. For example, you can type "reverse transcriptase" in input box and select species of "Nosema bombycis CQ1 v2", then click the Search button.
All posted SilkPathDB contents can be searched by the Web Page Search tool on the left block of home page. For example, you can search all contents related to "Nosema" by entering keyword "nosema" and clicking the Search button.
- Browse SilkPathDB pathogen genome
- Major analysis and tools
- Sequence search and anlignment. A powerful SilkPathDB BLAST engine was built from NCBI BLAST+, NCBI BLAST and AB-BLAST. Users can search and align sequences in a very easy way and get very readable results for further analysis. Furthermore, SilkPathDB BLAST supports search against multiple databases simultaneously.
- Search Gene Ontology. Users can search the GO information of a sequence using SilkPathDB Search GO tool with a given sequence or sequence id.
- Browse Gene Ontology. All genes of SilkPathDB pathogens were annotated for gene ontology iformation, from which we built the Silkworm Pathogen Gene Ontology browser - SilkPathGO, providing a global view on gene ontologies of SilkPathDB pathogens.
- Predict secreted protein. Secreted proteins are important factors to the infection of pathogen. A combined pipeline, EuSecPred, was developed to predict secreted proteins of eukaryotic pathogens. And ProSecPred was built to find secreted proteins of prokaryotic pathogens.
- SilkPathDB maintainance
The SilkPathDB is maintained by State Key Laboratory of Silkworm Genome Biology (SKLSGB), Southwest University (SWU), China. We keep on collecting and adding new species, omics data, experimental data of pathogens infecting silkworm and other Lepidoptera insects to SilkPathDB. We welcome people to share their data with SilkPathDB, as well as suggestions and advices on how to improve the SilkPathDB. Any questions please contact us.
- Cite SilkPathDB
Tian Li, Guo-Qing Pan, Charles R. Vossbrinck, Jin-Shan Xu, Chun-Feng Li, Jie Chen, Meng-Xian Long, Ming Yang, Xiao-Fei Xu, Chen Xu, Bettina A. Debrunner-Vossbrinck, Ze-Yang Zhou. SilkPathDB: a comprehensive resource for the study of silkworm pathogens. Database. 2017(1): bax001.