vardb.org
varDB: Antigenic variation databaseDatabase of gene families involved in antigenic variation
http://www.vardb.org/
Database of gene families involved in antigenic variation
http://www.vardb.org/
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Susumu Goto
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U●i , Kyoto, 611-0011
JP
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Susumu Goto
Go●●ho
U●i , Kyoto, 611-0011
JP
View this contact
Susumu Goto
Go●●ho
U●i , Kyoto, 611-0011
JP
View this contact
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varDB: Antigenic variation database | vardb.org Reviews
https://vardb.org
Database of gene families involved in antigenic variation
vardb.org
varDB Help
http://www.vardb.org/vardb/help/index.html
Create a user account. Report an error or comment. Use Blast to find similar sequences. Download sequences in FASTA formats. Create a user account. All features can be used without creating an account, but to save your search history and workspaces for later visits, a username and password can be easily created. To create a user account, click the "New account" link at the top right of each page. Report an error or comment. Use Blast to find similar sequences. Download sequences in FASTA formats.
Gene families
http://www.vardb.org/vardb/families.html
The following gene families were compiled based on literature searches, genome sequence projects, and Pfam profiles. The definition of antigenic variation differs slightly between eukaryotes, bacteria, and viruses. In eukaryotic species we selected families consisting of multiple paralogous genes with coordinated control of expression. In bacteria and viruses, we also include gene families that may include only one copy per individual but which participate in clonal variation. Uji, Kyoto 611-0011, Japan.
Alignments
http://www.vardb.org/vardb/alignments.html
Institute for Chemical Research. Uji, Kyoto 611-0011, Japan. System last updated Thu, January 24, 2013 14:25:29 JST / SVN revision: 1054.
PHI-BLAST
http://www.vardb.org/vardb/blast/phiblast.html
PHI-BLAST searches protein sequences using a combination of pattern matching and local alignment to reduce the probability of false positives. Institute for Chemical Research. Uji, Kyoto 611-0011, Japan. System last updated Thu, January 24, 2013 14:25:29 JST / SVN revision: 1054.
Netblast
http://www.vardb.org/vardb/analysis/netblast.html
Perform a remote BLAST search on sequences at NCBI using netblast. Institute for Chemical Research. Uji, Kyoto 611-0011, Japan. System last updated Thu, January 24, 2013 14:25:29 JST / SVN revision: 1054.
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Laboratory of Chemical Life Science - Research Projects
http://cls.kuicr.kyoto-u.ac.jp/projects.html
Laboratory of Chemical Life Science - Research Projects. Development of new bioinformatics technologies. Graph comparison and feature detection algorithms. Kernel methods for graph/network analysis. Gene expression profile analysis. Protein 3D structure prediction. List of GIW poster presentations. List of publications in Japanese. Kyoto Encyclopedia of Genes and Genomes. GenomeNet integrated database retrieval system. Genome and chemical analysis. Institute for Chemical Research.
GenomeNet - Bioinformatics Tools
http://www.genome.jp/en/gn_tools.html
The bioinformatics tools in the following three categories are available at GenomeNet. Except the standard programs for sequence similarity search and multiple sequence alignment, the tools have been developed by the Kyoto University Bioinformatics Center. Multiple sequence alignment and phylogenetic analysis. Query interface for KEGG OC (KEGG Ortholog Cluster). Nakaya et al. (2013). Automatic genome annotation (KO assignment) and pathway/brite mapping. Moriya et al. (2007). Takami et al. (2012).
GenomeNet - DBGET
http://www.genome.jp/en/gn_dbget.html
DBGET: Integrated Database Retrieval System. How to use DBGET/LinkDB. URLs for making DBGET queries. Growth of Major Databases (Compiled by Kanehisa Lab.). Kyoto University Bioinformatics Center.
GenomeNet - Other Tools
http://www.genome.jp/en/gn_kubic.html
Other Tools Developed by Kyoto University Bioinformatics Center. The following tools have also been developed by the Kyoto University Bioinformatics Center. They are maintained by the individual laboratories. Shimizu et al. (2011). A web tool for phage display analysis. Huang et al. (2006). Predict Half-Sphere Exposure from protein sequences. Song et al. (2008). Prediction of protein folding rates. Song et al. (2010). Subcellular Location Prediction with Frequency and Alignment. Tamura and Akutsu (2007).
GenomeNet - Database Release Information
http://www.genome.jp/en/info_dbget.html
Kyoto University Bioinformatics Center.
GenomeNet - FTP
http://www.genome.jp/en/gn_ftp.html
The GenomeNet FTP site provides freely available source codes of GenomeNet Bioinformatics tools and databases. DBGET database retrieval system [ FTP site. Download DBGET by [ FTP. Chemical structure search tools [ FTP site. SIMCOMP for similarity search [ FTP. SUBCOMP for substructure search [ FTP. KCFCO for converting mol to kcf format [ FTP. Gene expression profile database. Kyoto University Bioinformatics Center.
GenomeNet - Acknowledgments
http://www.genome.jp/en/acknowledge.html
GenomeNet acknowledges the use of the following databases. National Center for Biotechnology Information. National Institute of Genetics, Japan. Swiss Institute of Bioinformatics. National Biomedical Research Foundation. Research Collaboratory for Structural Bioinformatics. Institute for Protein Research, Osaka University, Japan. Swiss Institute for Experimental Cancer Center. Max Planck Institute for Marine Microbiology. CNRS/Station Biologique de Roscoff, France. CAMERA Data Distribution Center.
GenomeNet - Release Notes
http://www.genome.jp/en/release.html
October 8, 2016. Is updated (8 October version). 4,277 organisms (87 additional organisms from the previous release on 17 June) are included with more domain common clusters. July 1, 2016. Based on RefSeq release 75 now includes genomes listed in EBI Genomes. FTP download is also available. Is updated (17 June version). 4,190 organisms (130 additional organisms from the previous release on 16 January) are included with more domain common clusters. April 21, 2016. April 1, 2016. February 1, 2016. Is relea...
GenomeNet - Community Databases
http://www.genome.jp/en/gn_orfdb.html
The Kyoto University Bioinformatics Center has been in collaboration with groups of experimental laboratories for the development and maintenance of the following community databases. Cyanobacteria Gene Annotation Database. Bacillus subtilis Genome Database. Microarray Gene Expression Profile Database. Members of the Kyoto University Bioinformatics Center have developed the following databases as part of their research activities. Amino Acid Index Database. Kawashima et al. (2008). Okuda et al. (2006).
June | 2009 | Malaria Bulletin
https://malariabulletin.wordpress.com/2009/06
From Environmental Health at USAID. Environmental Health at USAID. Archive for June, 2009. Malaria Bulletin Update, June 16-30, 2009. June 30, 2009. This Malaria Bulletin update has citations and abstracts to 48 recently published. Malaria studies. Studies are listed alphabetically by journal title. 1: Acta Trop. 2009 Aug;111(2):197-9. Epub 2009 Apr 11. The suitability of clay pots for indoor sampling of mosquitoes in an arid area in. R, Takken W, Bousema T. Sample different populations of mosquitoes....
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varDB: Antigenic variation database
VarDB: Antigenic variation database. Many phylogenetically diverse organisms use antigenic variation. Sequences by country: 1. Number of GenBank antigenic variation field isolate sequences by country (extracted from the GenBank country field). The two chromosomes in (A). Encode different polypeptides. A recombination event ocurring in the first exon allows the generation of diversity (B). This website was developed as part of a collaboration between Kyoto University. In Japan and the Karolinska Institute.
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