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Vector-Parasite Genomic Related Databases

Vector-Parasite Genomic Related Databases. Chuong Huynh NIH/NLM/NCBI New Delhi, India Sept 29, 2004 huynh@ncbi.nlm.nih.gov. Suggested Reading?. Paper#1: Getting the Most Out of Bioinformatics Resources – Jessica Kissinger and David Roos

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Vector-Parasite Genomic Related Databases

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  1. Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI New Delhi, India Sept 29, 2004 huynh@ncbi.nlm.nih.gov

  2. Suggested Reading? • Paper#1: Getting the Most Out of Bioinformatics Resources – Jessica Kissinger and David Roos • Paper#2: Parasite Genome Databases and Web-based Resources – Christiane Hertz-Fowler and Neil Hall • Nucleic Acid Research Database Issue – Free Issue • Nucleic Acid Research Web Server Issue – Free Issue

  3. The 10 WHO/TDR Targetted Diseases • African trypanosomiasis • Dengue • Leishmaniasis • Malaria • Schistosomiasis • Tuberculosis • Chagas disease • Leprosy • Lymphatic filariasis • Onchocerciasis

  4. Participants • Malaria – 6 + 3 (part-time) • Schisto – 1 + 1 (part-time) • Toxoplasma - • Leishmania – 2 (part-time) • Anopheles – 1 • TB – 3 • Virus - 1 • No specific organism – 1 • Not available - 2

  5. GOLD – Genome OnLine Database • Resource for complete and ongoing genome projects around the world. http://www.genomesonline.org/

  6. General DNA/Protein Databases • Primary DNA and Protein Databases • EMBL/DDBJ/GenBank – nucleotide sequence submission/search/retrieval • TrEMBL – protein sequence database of translated nucleotide sequences • SWISS-PROT – manually annotated protein db • TrEMBL/SWISS-PROT/PIR  UniProt • InterPro – resource integrating protein signature db • CDD – conserved domain database

  7. Toward Organism Specific Genome Databases • GMOD - Generic Model Organism Database Construction Set • Genomics Unified Schema (GUS) - Based Genome Databases

  8. GMOD • Generic Model Organism Database Construction Set • http://www.gmod.org/ • a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology. • Based on Perl • E.g GiardiaDB

  9. GiardiaDB http://www.mbl.edu/Giardia

  10. GUS-Based Genome Databases • Genomics Unified Schema • Existing database schema for functional genomics and user interface • http://www.gusdb.org/ • Include: GeneDB, PlasmoDB, RAD, Allgenes, TcruziDB, CryptoDB, ToxoDB • Consistency; don’t have to reinvent the wheel, reusable components • Somewhat consistent user interface, pre-canned queries via e.g. scroll down forms

  11. GUS-Based Database

  12. Sanger Institute Pathogen Sequencing Unit http://www.sanger.ac.uk/Projects/Protozoa/ Team: http://www.sanger.ac.uk/Teams/Pathogen/

  13. Pathogen Sequencing Projectsat TIGR http://www.tigr.org/ http://www.tigr.org/faculty/

  14. Databases for Malaria

  15. Where do I find Plasmodium genome data? 1. TIGR and Sanger websites:or e-mail them !!! www.tigr.org

  16. TIGR Gene Indices home page http://www.tigr.org/tdb/tgi/ Newest addition…

  17. Sanger Institute: GeneDB http://www.genedb.org/

  18. 2. PlasmoDB http://PlasmoDB.org

  19. Malaria - Plasmodium Malaria Genome Sequencing Project Consortium Database http://plasmodb.org/

  20. PlasmoDB Feature • Searching PlasmoDB via text search, find genes by location, sequence features, path assignment, phylogenetic profile of orthologs, search and browse organeller genomes, boolean operators to combine search, sequence search, search gene expressionprofiles, search pathways and cellular location, • Browse sequence features such as AT content, tandem repeats, homology to other species of Plasmodium, EST similarities, and BLAST hits • Browse annotated features with links to detailed features and analysis • Provided gene features such as protein features, database cross references with with RefSeq, GenBank, provides access to automatically generated links to orthologous genes from several species • Bulk download in various formats of annotated and predicted gene sequences, translations, whole genomic sequences, and EST libraries

  21. 3. GenBank * Genomes & Maps * dbEST * dbGSS * nr * Malaria Genetics & Genomics

  22. Databases for Vectors

  23. AnoBase http://www.anobase.org/

  24. Ensembl - Mosquito • http://www.ensembl.org/Anopheles_gambiae/

  25. WHO/TDR Science Mosquito Genome CD

  26. NCBI MapViewer - Anopheles

  27. Mosquito Genome WWW Server http://mosquito.colostate.edu/tikiwiki/tiki-index.php

  28. Databases for “Parasites”

  29. http://www.nematodes.net/ Nematode Genomics

  30. Schistosoma mansoni http://verjo18.iq.usp.br/schisto/

  31. Leishmania major (Friedlin) • http://www.genedb.org/genedb/leish/index.jsp

  32. Trypanosoma brucei • http://www.genedb.org/genedb/tryp/index.jsp

  33. Trypanosoma cruzi • http://tcruzidb.org/

  34. Toxoplasma gondii • http://toxodb.org/

  35. Mycobacterium tuberculosis • http://genolist.pasteur.fr/TubercuList/

  36. M. Tuberculosis http://www.sanger.ac.uk/Projects/M_tuberculosis/ http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=gmt

  37. Microbial Genomes http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html

  38. Viruses http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/ICTVindex.htm

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