1. NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov

2. NCBI Did you read? 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 Participants Tse-tse fly -1 Malaria – 4 Tryp – 3 Toxoplasma - 1 Leishmania 2 Anopheles – 1 TB – 3 Dengue 1 No specific organism - 3

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

5. 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

6. 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

7. 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

8. NCBI GUS-Based Database

9. NCBI Databases for Vectors

10. 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

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

12. NCBI Ensembl - Anopheles http://www.ensembl.org/

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

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

15. NCBI Databases for “Parasites”

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

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

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

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

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

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

22. 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

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

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

25. 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

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

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

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

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

30. NCBI Extra slides

31. 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/

32. NCBI NCBI SNP Database Schema ftp://ftp.ncbi.nih.gov/snp/mssql/schema/erd_dbSNP.pdf