DemaDb: an integrated dematiaceous fungal genomes database
| Autor: | Soon-Joo Yap, Yue Fen Toh, Wai-Yan Yee, Su Mei Yew, Kok Wei Lee, Kee Peng Ng, Chai Ling Chan, Chee-Choong Hoh, Wei-Hien Cheong, Chee Sian Kuan |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Gene prediction 030106 microbiology Genes Fungal Genome browser Biology computer.software_genre Genome General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Databases Genetic Humans KEGG Gene Genetics Internet Database Models Genetic Molecular Sequence Annotation 030104 developmental biology Original Article Genome Fungal General Agricultural and Biological Sciences Functional genomics computer Information Systems InterProScan |
| Zdroj: | Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| Popis: | Many species of dematiaceous fungi are associated with allergic reactions and potentially fatal diseases in human, especially in tropical climates. Over the past 10 years, we have isolated more than 400 dematiaceous fungi from various clinical samples. In this study, DemaDb, an integrated database was designed to support the integration and analysis of dematiaceous fungal genomes. A total of 92 072 putative genes and 6527 pathways that identified in eight dematiaceous fungi (Bipolaris papendorfii UM 226, Daldinia eschscholtzii UM 1400, D. eschscholtzii UM 1020, Pyrenochaeta unguis-hominis UM 256, Ochroconis mirabilis UM 578, Cladosporium sphaerospermum UM 843, Herpotrichiellaceae sp. UM 238 and Pleosporales sp. UM 1110) were deposited in DemaDb. DemaDb includes functional annotations for all predicted gene models in all genomes, such as Gene Ontology, EuKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam and InterProScan. All predicted protein models were further functionally annotated to Carbohydrate-Active enzymes, peptidases, secondary metabolites and virulence factors. DemaDb Genome Browser enables users to browse and visualize entire genomes with annotation data including gene prediction, structure, orientation and custom feature tracks. The Pathway Browser based on the KEGG pathway database allows users to look into molecular interaction and reaction networks for all KEGG annotated genes. The availability of downloadable files containing assembly, nucleic acid, as well as protein data allows the direct retrieval for further downstream works. DemaDb is a useful resource for fungal research community especially those involved in genome-scale analysis, functional genomics, genetics and disease studies of dematiaceous fungi. Database URL: http://fungaldb.um.edu.my. |
| Databáze: | OpenAIRE |
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