Genomics databases
From MyBio
Also see Genetics databases
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[edit] Genomics databases - Quick Links
| STD Sequence Databases | DoTS | |
| ACeDB | GeneDB | |
| EPConDB | HuGeMap | |
| ORFanage | Virgil | |
| ZFIN | Genome Databases in Japan | |
| The Sanger Institute: AceDB Database |
[edit] Genomics databases - Web Resources
STD Sequence Databases
STDGEN. Molecular information pertaining to sexually transmitted bacteria and viruses, but is not limited to molecular sequence data. Focus is upon the sequenced genomes of Chlamydia pneumoniae, Chlamydia trachomatis, Mycoplasma genitalium, Treponema pallidum, Ureaplasma urealyticum, as well as Human Papillomavirus. Between 2000 and 2003 Human Herpesvirus 1 (HSV-1), Human Herpesvirus 2 (HSV-2), Human Herpesvirus 8 (KSHV) and Human Herpesvirus 5 (HCMV) were added one each year. Also in 2002 Neisseria gonorrhoeae was added. 2003 additions include Streptococcus agalactiae and Haemophilus ducreyi.
DoTS
Database Of Transcribed Sequences. Human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index.
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ACeDB
C. elegans, S. pombe, and human sequences and genomic information.
GeneDB
Resource for prokaryotic and eukaryotic organisms. GeneDB is a genome database for prokaryotic and eukaryotic organisms. The resource provides a portal through which data generated by the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be made publicly available. It combines data from finished and ongoing genome and expressed sequence tag (EST) projects with curated annotation, that can be searched, sorted and downloaded, using a single web based resource. The current release stores 11 datasets of which six are curated and maintained by biologists, who review and incorporate information from the scientific literature, public databases and the respective research communities.
EPConDB
Endocrine Pancrease Consortium. EPConDB contains information on genes expressed in cells of the pancreas identified by dbEST libraries from pancreatic tissues including the 12 mouse and 7 human libraries generated by the Endocrine Pancreas Consortium. Pancreatic genes were also identified by microarray analysis of pancreatic tissues. Microarray chips based on these pancreatic genes (PancChip) have been developed. These chips are described and results of their usage presented.
HuGeMap
Human genome map. HuGeMap is a database that contains the genetic maps from Généthon, the genetic maps from Cooperative Human Linkage Center, the physical maps from CEPH/Généthon and the physical maps from the Whitehead Institute-MIT.
ORFanage
ORFan database (db of orphan ORF, or ORFs that have no matches with other ORFs). As each newly sequenced genome contains a significant number of protein-coding ORFs that are species-, family- or lineage-specific, many interesting questions arise about the evolution and role of these ORFs and of the genomes they are part of. We refer to these poorly conserved ORFs as singleton or paralogous ORFans if they are unique to one genome, or as orthologous ORFans if they appear only in a family of closely related organisms and have no homolog in other genomes. In order to study and classify ORFans we have constructed the ORFanage, an ORFan database. This database consists of the predicted ORFs in fully sequenced microbial genomes, and enables searching for the three types of ORFans in any subset of the genomes chosen by the user. The ORFanage could help in choosing interesting targets for further genomic and evolutionary studies.
Virgil
Human oriented database interlinking several databases including GenBank and SWISS-PROT. Virgil is a database of rich links for data browsing, data analysis and database interconnection, with a focus on human data. It contains more than 40000 rich links from 5 major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM.
ZFIN
Zebrafish information network. ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community
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Genome Databases in Japan
Genome Databases in Japan BSORF: Bacillus subtilis Genome Database. Bioinformatics Center, Kyoto University and Nara Institute of Science and Technology CYORF: Cyanobacteria Community Annotation Database. Bioinformatics Center, Kyoto ...
The Sanger Institute: AceDB Database
Sanger Home. Acedb. YourGenome. Ensembl. Trace Server. Library. Data Release Policy. Conditions of Use. Introduction. Quick Guide. Showcase. Sanger Databases. AceDB newsgroup. News letters. Future plans. AceDB is a genome database designed ...
