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The Fungal Secretome KnowledgeBase (FunSecKB) provides a resource of secreted fungal proteins, i.e. secretomes, identified from all available fungal protein data in the NCBI RefSeq database. The secreted proteins were identified using a well evaluated computational protocol which includes SignalP, WolfPsort and Phobius for signal peptide or subcellular location prediction, TMHMM for identifying membrane proteins, and PS-Scan for identifying endoplasmic reticulum (ER) target proteins. The entries were mapped to the UniProt database and any annotations of subcellular locations that were either manually curated or computationally predicted were included in FunSecKB. Using a web-based user interface, the database is searchable, browsable and downloadable by using NCBI's RefSeq accession or gi number, UniProt accession number, keyword or by species. A BLAST utility was integrated to allow users to query the database by sequence similarity. A user submission tool was implemented to support community annotation of subcellular locations of fungal proteins. With the complete fungal data from RefSeq and associated web-based tools, FunSecKB will be a valuable resource for exploring the potential applications of fungal secreted proteins. Database URL: http://proteomics.ysu.edu/secretomes/fungi.php.
Pubmed ID: 21300622 RIS Download
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Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
View all literature mentionsThe Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.
View all literature mentionsService to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs.
View all literature mentionsA sister database to ProSite, is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format. In addition to these rules corresponding to a unique PROSITE motif, there are also rules triggered by a specific combination of PROSITE motifs called metamotifs. Metamotifs allow the definition of arrangements of domains separated by spacers of variable size, as well as the anchoring to the N- and/or C-termini and the exclusion of a PROSITE motif. ProRule uses the UniRule format that is common to all types of rules created to annotate UniProtKB/Swiss-Prot, including the HAMAP family rules. Each rule contains information used to provide template based annotation associated with the domain or family detected by the PROSITE motif. ProRule is used to create UniProtKB/Swiss-Prot lines with basic and complex annotation derived from the presence of the domain and of biologically critical amino acids: domain name and boundaries, EC number, function, keywords, associated PROSITE patterns, PTMs, active sites, disulfide bonds, etc.). ProRule contains notably the position of structurally and/or functionally critical amino acid(s), as well as the condition(s) they must fulfil to play their biological role(s). Part of these supplementary data are used by ScanProsite that not only provides the protein sequence matched by a profile, but also information about the relevance of biologically meaningful residues, like active sites, binding sites, post-translational modification sites or disulfide bonds, to help function determination
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