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

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

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

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

8. NCBI 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. WormBaseFlyBaseMGISGDGrameneRat Genome DatabaseEcoCycTAIR Based on Perl E.g GiardiaDB

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

10. NCBI 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. NCBI GUS-Based Database

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

13. NCBI Pathogen Sequencing Projects at TIGR http://www.tigr.org/faculty/ http://www.tigr.org/

14. NCBI Databases for Malaria

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

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

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

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

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

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

22. NCBI Databases for Vectors

23. NCBI Mosquito Resources 1. AnoBase - the Anopheles database http://www.anobase.org/ 2. Anopheles Gene Plot Cd-rom You should have this, but a local copy is available on the course website. 3.http://www.ensembl.org/Anopheles_gambiae/ 4.http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi? taxid=7165

24. NCBI AnoBase http://www.anobase.org/

25. NCBI Ensembl - Mosquito http://www.ensembl.org/Anopheles_gambiae/

26. NCBI WHO/TDR Science Mosquito Genome CD

27. NCBI NCBI MapViewer - Anopheles

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

29. NCBI Tse-tse (Glossina) Fly http://www.genedb.org/genedb/glossina/index.jsp

30. NCBI Databases for “Parasites”

31. NCBI http://www.nematodes.net/ Nematode Genomics

32. NCBI Schistosoma mansoni http://verjo18.iq.usp.br/schisto/

33. NCBI Leishmania major (Friedlin) http://www.genedb.org/genedb/leish/index.jsp

34. NCBI Trypanosoma brucei http://www.genedb.org/genedb/tryp/index.jsp

35. NCBI Trypanosoma cruzi http://tcruzidb.org/

36. NCBI Toxoplasma gondii http://toxodb.org/

37. NCBI Mycobacterium tuberculosis http://genolist.pasteur.fr/TubercuList/

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

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

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

41. NCBI Extra slides

42. NCBI Entamoeba E. histolytica 7X assembly Feb 2003 E. terrapinae E. invadens 2.8 X coverage March 2003 E. moshkovskii http://homepages.lshtm.ac.uk/entamoeba/

43. NCBI Giardia lamblia 11.7 Mbp genome 355 contigs as of July 2004 (143 supercontigs) 95.93% coverage GiardiaDB –uses Generic Model Organism Database http://www.mbl.edu/Giardia