ncbi vector-parasite genomic related databases chuong huynh nih/nlm/ncbi sao paulo, brasil july 12,...
TRANSCRIPT
![Page 1: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/1.jpg)
NC
BI
Vector-Parasite Genomic
Related DatabasesChuong HuynhNIH/NLM/NCBI
Sao Paulo, BrasilJuly 12, 2004
![Page 2: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/2.jpg)
NC
BI
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
![Page 3: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/3.jpg)
NC
BI
Participants
• Tse-tse fly -1• Malaria – 4• Tryp – 3• Toxoplasma - 1• Leishmania 2• Anopheles – 1• TB – 3• Dengue 1• No specific organism - 3
![Page 4: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/4.jpg)
NC
BI
GOLD – Genome OnLine Database
• Resource for complete and ongoing genome projects around the world.
http://www.genomesonline.org/
![Page 5: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/5.jpg)
NC
BI
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
![Page 6: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/6.jpg)
NC
BI
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
![Page 7: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/7.jpg)
NC
BI
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
![Page 8: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/8.jpg)
NC
BI
GUS-Based Database
![Page 9: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/9.jpg)
NC
BI
Databases for Vectors
![Page 10: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/10.jpg)
NC
BI
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
![Page 11: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/11.jpg)
NC
BI
AnoBase
http://www.anobase.org/
![Page 12: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/12.jpg)
NC
BI
Ensembl - Anopheles
http://www.ensembl.org/
![Page 13: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/13.jpg)
NC
BI
Mosquito Genome WWW Server
http://mosquito.colostate.edu/tikiwiki/tiki-index.php
![Page 14: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/14.jpg)
NC
BI
Databases for “Parasites”
![Page 15: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/15.jpg)
NC
BI
http://www.nematodes.net/
Nematode Genomics
![Page 16: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/16.jpg)
NC
BI
Schistosoma mansoni
http://verjo18.iq.usp.br/schisto/
![Page 17: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/17.jpg)
NC
BI
Leishmania major (Friedlin)
• http://www.genedb.org/genedb/leish/index.jsp
![Page 18: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/18.jpg)
NC
BI
Trypanosoma brucei
• http://www.genedb.org/genedb/tryp/index.jsp
![Page 19: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/19.jpg)
NC
BI
Trypanosoma cruzi
• http://tcruzidb.org/
![Page 20: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/20.jpg)
NC
BI
Malaria - Plasmodium
Malaria Genome Sequencing Project Consortium Database
http://plasmodb.org/
![Page 21: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/21.jpg)
NC
BI
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
![Page 22: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/22.jpg)
NC
BI
Toxoplasma gondii
• http://toxodb.org/
![Page 23: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/23.jpg)
NC
BI
Mycobacterium tuberculosis
• http://genolist.pasteur.fr/TubercuList/
![Page 24: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/24.jpg)
NC
BI
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
![Page 25: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/25.jpg)
NC
BI
GiardiaDB
http://www.mbl.edu/Giardia
![Page 26: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/26.jpg)
NC
BI
M. Tuberculosis
http://www.sanger.ac.uk/Projects/M_tuberculosis/http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?
database=gmt
![Page 27: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/27.jpg)
NC
BI
Microbial Genomes
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html
![Page 28: NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004 huynh@ncbi.nlm.nih.gov](https://reader030.vdocuments.mx/reader030/viewer/2022032607/56649ed25503460f94be2905/html5/thumbnails/28.jpg)
NC
BI
Viruses
http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/ICTVindex.htm