ncbi vector-parasite genomic related databases chuong huynh nih/nlm/ncbi sao paulo, brasil july 12,...

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Vector-Parasite Genomic

Related DatabasesChuong HuynhNIH/NLM/NCBI

Sao Paulo, BrasilJuly 12, 2004

huynh@ncbi.nlm.nih.gov

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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

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Participants

• Tse-tse fly -1• Malaria – 4• Tryp – 3• Toxoplasma - 1• Leishmania 2• Anopheles – 1• TB – 3• Dengue 1• No specific organism - 3

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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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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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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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Databases for Vectors

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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

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AnoBase

http://www.anobase.org/

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Ensembl - Anopheles

http://www.ensembl.org/

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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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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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Toxoplasma gondii

• http://toxodb.org/

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Mycobacterium tuberculosis

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

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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

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GiardiaDB

http://www.mbl.edu/Giardia

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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