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Vector-Parasite Genomic
Related Databases
NCBI
Chuong Huynh
NIH/NLM/NCBI
New Delhi, India
Sept 29, 2004
[email protected]
Suggested Reading?
NCBI
• 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
The 10 WHO/TDR Targetted Diseases
African trypanosomiasis
Dengue
Leishmaniasis
Malaria
Schistosomiasis
Tuberculosis
Chagas disease
Leprosy
Lymphatic filariasis
Onchocerciasis
NCBI
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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
NCBI
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GOLD – Genome OnLine Database
• Resource for complete and ongoing genome
projects around the world.
NCBI
http://www.genomesonline.org/
General DNA/Protein Databases
• Primary DNA and Protein Databases
NCBI
– 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
Toward Organism Specific
Genome Databases
• GMOD - Generic Model Organism
Database Construction Set
• Genomics Unified Schema (GUS) - Based
Genome Databases
NCBI
GMOD
NCBI
• 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
GiardiaDB
NCBI
http://www.mbl.edu/Giardia
GUS-Based Genome Databases
NCBI
• 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, precanned queries via e.g. scroll down forms
GUS-Based Database
NCBI
Sanger Institute
Pathogen Sequencing Unit
http://www.sanger.ac.uk/Projects/Protozoa/
Team: http://www.sanger.ac.uk/Teams/Pathogen/
NCBI
Pathogen Sequencing Projects
at TIGR
http://www.tigr.org/
http://www.tigr.org/faculty/
NCBI
Databases for Malaria
NCBI
Where do I find Plasmodium genome data?
1. TIGR and Sanger websites: or e-mail them !!!
www.tigr.org
NCBI
TIGR Gene Indices
home page
http://www.tigr.org/tdb/tgi/
NCBI
Newest addition…
Sanger Institute: GeneDB
http://www.genedb.org/
NCBI
2. PlasmoDB
http://PlasmoDB.org
NCBI
Malaria - Plasmodium
Malaria Genome Sequencing Project Consortium Database
NCBI
http://plasmodb.org/
PlasmoDB Feature
NCBI
• 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
3. GenBank
* Genomes & Maps
* dbEST
* dbGSS
* nr
* Malaria
Genetics &
Genomics
NCBI
Databases for Vectors
NCBI
AnoBase
NCBI
http://www.anobase.org/
Ensembl - Mosquito
NCBI
• http://www.ensembl.org/Anopheles_gambiae/
WHO/TDR Science Mosquito Genome CD
NCBI
NCBI MapViewer - Anopheles
NCBI
Mosquito Genome WWW Server
NCBI
http://mosquito.colostate.edu/tikiwiki/tiki-index.php
Databases for “Parasites”
NCBI
Nematode Genomics
NCBI
http://www.nematodes.net/
Schistosoma mansoni
NCBI
http://verjo18.iq.usp.br/schisto/
Leishmania major (Friedlin)
NCBI
• http://www.genedb.org/genedb/leish/index.jsp
Trypanosoma brucei
NCBI
• http://www.genedb.org/genedb/tryp/index.jsp
Trypanosoma cruzi
NCBI
• http://tcruzidb.org/
Toxoplasma gondii
NCBI
• http://toxodb.org/
Mycobacterium tuberculosis
NCBI
• http://genolist.pasteur.fr/TubercuList/
M. Tuberculosis
NCBI
http://www.sanger.ac.uk/Projects/M_tuberculosis/
http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=gmt
Microbial Genomes
NCBI
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html
Viruses
NCBI
http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/ICTVindex.htm