VectorParasite Genomic Related Databases NCBI Chuong Huynh NIHNLMNCBI

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

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 • • •

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 • • •

GOLD – Genome On. Line 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/Gen. Bank – nucleotide sequence submission/search/retrieval – Tr. EMBL – protein sequence database of translated nucleotide sequences – SWISS-PROT – manually annotated protein db – Tr. EMBL/SWISS-PROT/PIR Uni. Prot – Inter. Pro – 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 Worm. Base, Fly. Base, MGI, SGD, Gramene, Rat Genome Database, Eco. Cyc, and TAIR to develop reusable components suitable for creating new community databases of biology. • Based on Perl • E. g Giardia. DB

Giardia. DB 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: Gene. DB, Plasmo. DB, RAD, Allgenes, Tcruzi. DB, Crypto. DB, Toxo. DB • 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/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: Gene. DB http: //www. genedb. org/ NCBI

2. Plasmo. DB http: //Plasmo. DB. org NCBI

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

Plasmo. DB Feature NCBI • Searching Plasmo. DB 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 Ref. Seq, Gen. Bank, 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