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PA-GOSUB: A searchable database of model organism protein sequences with their predicted GO molecular function and subcellular localization
Download2005
Poulin, B., Lu, P., Wishart, D.S., Szafron, D., Lamb, N., Eisner, R., Pearcy, B., Ngo, D., Fyshe, A., Grenier, R.
PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107 000 proteins...
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2004
Wishart, D.S., Stothard, P., Dong, X., Forsythe, I.
PlasMapper is a comprehensive web server that automatically generates and annotates high-quality circular plasmid maps. Taking only the plasmid/vector DNA sequence as input, PlasMapper uses sequence pattern matching and BLAST alignment to automatically identify and label common promoters,...
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PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Download2008
Stothard, P., Damaraju, S., Wishart, D.S., Young, N., Cheng, D., Knox, C.
A particular challenge in biomedical text mining is to find ways of handling ‘comprehensive’ or ‘associative’ queries such as ‘Find all genes associated with breast cancer’. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe...
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PROTEUS2: A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation
Download2008
Shrivistava, S., Berjanskii, M., Wishart, D.S., Cruz, J.A., Arndt, D., Montgomerie, S.
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary...
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The CyberCell Database (CCDB): A comprehensive, self-updating relational database to coordinate and facilitate in silico modeling of Escherichia coli
Download2004
Stothard, P., Rouani, M., Sundararaj, S., Wishart, D.S., Nazhad, B.H., Guo, A., Ellison, M.
The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data...