Links
"From the genome to the tree of life"
Publications Research Centers Databases Societies Software Deep Gene Participants

 Genetics / Genomics Databases          >>>Phylogentics Databases<<<
 
   Plant Databases:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ARS Genome Database Resource (Cornell)
ARS Genome Database Resource is primarily a site for communication of Plant Genome data among scientists worldwide. The medium is a set of genome databases, similar to the ones for Human genome mapping and sequencing. They include data about plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varieties that possess those traits.
 
CottonDB
A resource on the developing knowledge base of Cotton Genetics.
Dendrome, US TreeGenes
Dendrome is a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community
KOMUGI (Japan)
GrainGenes, a genome database for Triticeae and related species. RiceGenes a genome database for rice.

MaizeDB, US MaizeDB Database
A public Internet gateway to current knowledge about the maize genome and its expression.
Mendel Bioinformatics Group, UK
Mendel-ESTS, contains all of the plant EST and STS sequences currently in dbEST and dbSTS (>94,000) related to the sequences, grouped by gene family, in the Gene Family Database.
Mendel-GFDb
Database of Genes Organized by Families. Now with Pfam, Prosite & TRANSFAC domain information
Plant Chromatin Database
Database for chromatin proteins in plants, including functions and molecular phylogenetic relationships, with initial emphasis on Arabidopsis and maize
 
RiceGAAS: Rice Genome Annotation Database
A rice genome automated annotation system; integrates programs for prediction and analysis of protein-coding gene structure.

SIU-C Soy Phytoestrogen Gene Mapping

Stanford Genomic Resources USA
SGD (Saccharomyces), scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae(baker's or budding yeast).
Mendel-CPGN
: developinging a common nomenclature for sequenced plant genes
SolGenes -- Genome Database for the Solanaceae
A U.S.D.A.-funded Genome Database for the Solanaceae, containing information about potatoes, tomatoes, peppers, and related species.
ZmDB Maize Genome Database
Goals include discovering maize genes using EST sequencing and engineered Mu (RescueMu) tagging, and developing new tools to facilitate gene mapping and phenotypic analysis.

   General and Non-plant Databases:
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ARCHAIC : ARCHAeobacterial Information Collection
The aim of ARCHAIC is to analyze archaebacterial genomic DNA sequences in order to understand the overall organization of these genomes and in order to permit comparison of different species on the basis of their genomic DNA sequences.

DNA Data Bank of Japan
DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters.

ExPASy Molecular Biology Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.

European Bioinformatics Institute
The European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
Genbank
This site allows you to search and download registered gene sequences, with information on the gene's function, and the organism in which it was found.
Genome Database of the Human Genome Project
GDB's mission is to make available to scientists an encyclopedia of the human genome that is being constantly revised and updated to reflect the current state of scientific knowledge.

National Center for Biotechnology Information / GenBank
NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.

National Center for Genome Resources
The National Center for Genome Resources links scientists to innovative solutions in bioinformatics — through collaborations, data management, and
creative software development.

Pfam Protein Domain Database
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
 
Sanger Centre Databases, UK
The Sanger Institute provides its own computing resources and database storage for public access by the scientific community.

National Center for Genome Resources ,
USA The National Center for Genome Resources links scientists to innovative solutions in bioinformatics — through collaborations, data management, and
creative software development.

Danish Server for Biology/Genome Science
The Johns Hopkins University BioInformatics Web Server
an encyclopedia of the human genome that is being constantly revised and updated to reflect the current state of scientific knowledge. Historically focussed on gene mapping but is moving from mapping to sequence to functional analysis.

 

 Phylogenetics Databases           [Genetics/Genomics Databases]
 
   General Databases
 

Tree of Life
Organized by the Maddisons, this is an attempt to have the entire phylogeny of life on earth (as currently understood) on-line and accessible to everyone. The site has many pages on fish and arthropods, with more coverage being added all the time.
 
TreeBASE
Fledgling project to establish a relational database of phylogenetic information, especially published trees and data matrices. The project has begun by concentrating on green plant data (particularly angiosperms), but hopes to eventually include studies on all organisms, based on all types of data.
UCMP Phylogeny Exhibit
Educational exhibit on the major groups of life on earth, with information about the fossil record, ecology, morphology, and systematics of each group. Also try the UCMP WebLift to Taxa, which is an index to all groups currently treated.

   Molecular Databases
 

 

 

 

 

 

 

 

Genbank
This site allows you to search and download registered gene sequences, with information on the gene's function, and the organism in which it was found.
 
Image Library of Biological Macromolecules (IMB Jena)
Includes RNA and protein structures, some with VRML versions
 
Immunogenetics Database
International database specializing in immunoglobulins, T-cell receptors, and major histocompatibility complex molecules of all vertebrate species
 
Oligonucleotide Probe Database
Downloadable data, mailing list and discussion
 
Ribosomal Database Project (RDP-II)
Offers ribosome related data, analysis services, and software
 
SEQNET
Offers access to major sequence and molecular structure databases, as well as programs
 
SWISS-PROT
Annotated protein sequence database
 
Virus Sequences, Alignments, and Phylogenetic Trees

   Taxonomic Databases
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Approved Lists of Bacterial Names
Searchable database
 
Flora of North America
Information on the names, taxonomic relationships, continent-wide distributions, and morphological characteristics of all plants native and naturalized found in North America north of Mexico
 
Gray Herbarium Card Index
Searchable version of the valuable Gray Index, including New World vascular plant taxa at the level of species and below
 
Index Nominum Genericorum (Plantarum)
Searchable database of generic names for all organisms covered by the ICBN (International Code of Botanical Nomenclature), including bryophytes, algae, fungi, etc.
 
Index Virum
Collection of index files which link to lists on viral nomenclature.
 
Indices Nominum Supragenericorum Plantarum Vascularium
Searchable database for vascular plant taxa names above the generic level
 
International Organization for Plant Information

Internet Biodiversity Service
Includes the data for Species 2000, UNESCO, and IOP
Jepson Flora Project: Plants of California
Information on identification, taxonomy, distribution, ecology, relationships, and diversity of California vascular plants
Mammal Species of the World
Searchable database of all currently recognized species of (living) mammals, with data on each species
 
PLANTS Projects Databases
Collection of US databases of the North American flora. Includes the Interagency Taxonomic Information System (ITIS)
 
Species 2000
A British attempt to index the scientific names of all known species


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