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2008
Stothard, Paul. , Grant, Jason R.
The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the...
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2015
Stothard, Paul, Wang, Yining, Lin, Guohui, Wylie, Tim
Background Despite ongoing reductions in the cost of sequencing technologies, whole genome SNP genotype imputation is often used as an alternative for obtaining abundant SNP genotypes for genome wide association studies. Several existing genotype imputation methods can be efficient for this...
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2011
Liao, Xiaoping, Choi, Jung-Woo, Stothard, Paul, Basu, Urmila, Sumner-Thomson, Jennifer M., Meng, Yan, Moore, Stephen S.
Background One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or...
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2012
Stothard, Paul, Arantes, Adriano S., Grant, Jason R.
Background Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the...
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2006
Chang, Zhan, Hassanali, Murtaza, Wishart, David S., Stothard, Paul, Woolsey, Jennifer, Guo, AnChi, Shrivistava, Savita, Knox, Craig
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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2012
Wishart, David S., Cruz, Joseph, Tang, Peter, Stothard, Paul, Zhou, Jianjun, Berjanskii, Mark, Liang, Yongjie, Lu, Paul, Zhou, You, Lin, Gouhui, MacDonell, Cam
Originally released in 2005, BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains fully labeled, zoomable and searchable chromosome maps for essentially all sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level...
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2010-01-01
PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS...
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2005
Wishart, David S., Shrivastava, Savita, Ellison, Michael, Guo, Anchi, Cruz, Joseph, van Domselaar, Gary, O'Neill, Brian, Stothard, Paul
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 high-resolution circular genome maps from...
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PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Download2008
Cheng, Dean, Stothard, Paul, Damaraju, Sambasivarao, Wishart, David S., Knox, Craig, Young, Nelson
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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Development of a porcine (Sus scofus) embryo-specific microarray: Annotation and validation
Download2012
Dobrinsky, John, Zhou, Chi, Pasternak, J. Alexander, Dyck, Michael K., Foxcroft, George R., Nieminen, Julie, Tsoi, Stephen, Rigault, Philippe, Sirard, Marc-André, Robert, Claude, Grant, Jason R.
Background The domestic pig is an important livestock species and there is strong interest in the factors that affect the development of viable embryos and offspring in this species. A limited understanding of the molecular mechanisms involved in early embryonic development has inhibited our...