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Vector-Parasite Genomic

Related DatabasesChuong HuynhNIH/NLM/NCBI

New Delhi, IndiaSept 29, 2004

huynh@ncbi.nlm.nih.gov

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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

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The 10 WHO/TDR Targetted Diseases

• African trypanosomiasis • Dengue• Leishmaniasis• Malaria• Schistosomiasis• Tuberculosis• Chagas disease• Leprosy• Lymphatic filariasis• Onchocerciasis

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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

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GOLD – Genome OnLine Database

• Resource for complete and ongoing genome projects around the world.

http://www.genomesonline.org/

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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

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Toward Organism Specific

Genome Databases

• GMOD - Generic Model Organism Database Construction Set

• Genomics Unified Schema (GUS) - Based Genome Databases

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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

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GiardiaDB

http://www.mbl.edu/Giardia

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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

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GUS-Based Database

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Sanger Institute Pathogen Sequencing

Unithttp://www.sanger.ac.uk/Projects/Protozoa/

Team: http://www.sanger.ac.uk/Teams/Pathogen/

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Pathogen Sequencing Projectsat TIGR

http://www.tigr.org/faculty/

http://www.tigr.org/

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Databases for Malaria

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www.tigr.org

Where do I find Plasmodium genome data?

1. TIGR and Sanger websites: or e-mail them !!!

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TIGR Gene Indices home page

http://www.tigr.org/tdb/tgi/

Newest addition…

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Sanger Institute: GeneDB

http://www.genedb.org/

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http://PlasmoDB.org

2. PlasmoDB

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Malaria - Plasmodium

Malaria Genome Sequencing Project Consortium Database

http://plasmodb.org/

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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

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3. GenBank

* Genomes & Maps* dbEST* dbGSS* nr* Malaria Genetics & Genomics

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Databases for Vectors

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AnoBase

http://www.anobase.org/

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Ensembl - Mosquito

• http://www.ensembl.org/Anopheles_gambiae/

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WHO/TDR Science Mosquito Genome CD

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NCBI MapViewer - Anopheles

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Mosquito Genome WWW Server

http://mosquito.colostate.edu/tikiwiki/tiki-index.php

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Databases for “Parasites”

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http://www.nematodes.net/

Nematode Genomics

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Schistosoma mansoni

http://verjo18.iq.usp.br/schisto/

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Leishmania major (Friedlin)

• http://www.genedb.org/genedb/leish/index.jsp

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Trypanosoma brucei

• http://www.genedb.org/genedb/tryp/index.jsp

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Trypanosoma cruzi

• http://tcruzidb.org/

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Toxoplasma gondii

• http://toxodb.org/

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Mycobacterium tuberculosis

• http://genolist.pasteur.fr/TubercuList/

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M. Tuberculosis

http://www.sanger.ac.uk/Projects/M_tuberculosis/http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?

database=gmt

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Microbial Genomes

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

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Viruses

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