title: DemaDb: an integrated dematiaceous fungal genomes database.
abstract: 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.
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Chee Sian
authors.initials: CS
authors.lastname: Kuan
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Su Mei
authors.initials: SM
authors.lastname: Yew
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Chai Ling
authors.initials: CL
authors.lastname: Chan
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Yue Fen
authors.initials: YF
authors.lastname: Toh
authors.affiliation: Codon Genomics SB, No.26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200 Seri Kembangan, Selangor Darul Ehsan, Malaysia.
authors.forename: Kok Wei
authors.initials: KW
authors.lastname: Lee
authors.affiliation: Codon Genomics SB, No.26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200 Seri Kembangan, Selangor Darul Ehsan, Malaysia.
authors.forename: Wei-Hien
authors.initials: WH
authors.lastname: Cheong
authors.affiliation: Codon Genomics SB, No.26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200 Seri Kembangan, Selangor Darul Ehsan, Malaysia.
authors.forename: Wai-Yan
authors.initials: WY
authors.lastname: Yee
authors.affiliation: Codon Genomics SB, No.26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200 Seri Kembangan, Selangor Darul Ehsan, Malaysia.
authors.forename: Chee-Choong
authors.initials: CC
authors.lastname: Hoh
authors.affiliation: Codon Genomics SB, No.26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200 Seri Kembangan, Selangor Darul Ehsan, Malaysia.
authors.forename: Soon-Joo
authors.initials: SJ
authors.lastname: Yap
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia kpng@ummc.edu.my.
authors.forename: Kee Peng
authors.initials: KP
authors.lastname: Ng
mesh_terms: D030541:Databases, Genetic; D005800:Genes, Fungal; D016681:Genome, Fungal; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D058977:Molecular Sequence Annotation