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BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics
Download2004
Wang, J., Chen, Y., Zhao, H., Dai, M., Zhao, W., Huang, X., Zhang, Y., Ren. X., Jiao, Y., Wong, G., Wei, S., Ni, P., Yu, J., Zhang, J., Li, S., Yang, H., Fu, J., He, X.
Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate...
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2005
Stothard, P., Van Domselaar, G., Cruz, J., Wishart, D.S., Shrivistava, S., Guo, A.C., O'Neill, B., Ellison, M.J.
BacMap is an interactive visual database containing fully labeled, zoomable and searchable chromosome maps from more than 170 bacterial (archaebacterial and eubacterial) species. It uses a recently developed visualization tool (CGView) to generate highresolution circular genome maps from sequence...
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2005
Xia, Q., Chen, J., Dai, M., Ye, C., Wang, J., Li, S., Li, R., Zhou, Z., Ruan, J., Hu, Y., Yu, G., Yang, H., He, X., Yu, Jun, Xiang, Z., Yuan, H., Lu, C., Feng, T.
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ~6X draft genome sequence of the domestic silkworm (Bombyx mori ), SilkDB provides an integrated representation of the...
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2005
Stothard, P., Lu, P., Cruz, J.A., Szafron, D., Van Domselaar, G.H., Shrivistava, S., Guo, A., Dong, X., Grenier, R., Wishart, D.S.
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and...
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2006
Hassanali, M., Stothard, P., Knox, C., Wishart, D.S., Shrivastava, S., Guo, A., Woolsey, J.
DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains .4100 drug entries including .800 FDA approved small molecule and biotech drugs as well as .3200...
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Improving the accuracy of protein secondary structure prediction using structural alignment
Download2006
Gallin, W.J., Wishart, D.S., Montgomerie, S., Sundararaj, S.
Background: The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed...
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2006
Berlyn, M.K., Plunkett, G., Wishart, D.S., Nori, H., Riley, M., Rudd, K.E., Glasner, J.D., Arnaud, M.B., Abe, T., Thomson, N.R., Wanner, B.L., Pernas, N.T., Blattner, F.R., Serres, M.H., Thomas, G.H., Horiuchi, T., Kosuge, T., Keseler, I.M., Chaudhuri, R.R.
The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene...
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2007
Guan, L., Guo, Y., Liu, T., Li, H., Wang, J., Zheng, W.M., Wong, G.K.
Background The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...
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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...