model organisms
Arabidopsis | Caenorhabditis
elegans | Drosophila | Escherichia
coli | Medicago
trunculata | Mouse | Rat | Saccharomyces |
Xenopus | Zebrafish |
more
Arabidopsis
The Arabidopsis Information Resource (TAIR)
http://www.arabidopsis.org/
TAIR collects and provides access to an extensive collection of information
about Arabidopsis. TAIR maintains a database of genetic and molecular
biology data with information about genes, proteins, markers, and polymorphisms.
Other information includes publications, contacts for A. thaliana researches,
protocols, microarrays, and germplasm availability.
Genome Cluster Database
http://bioweb.ucr.edu/databaseWeb/index.jsp
Protein sequences derived from Arabidopsis are analyzed and clustered
into families. The database includes family name, protein alignments, and a
phylogenetic tree for each cluster. Underlying sequence data and tools for
data mining and analysis are also available.
PHYTOPROT (PHP)
http://urgi.versailles.inra.fr/phytoprot/
PHP is a database of Arabidopsis protein sequences clustered into
families based on sequence similarities. Families, subfamilies and domains
are identified for each cluster.
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Caenorhabditis elegans
Caenorhabditis elegans Genome and Genomics
http://elegans.swmed.edu/genome.shtml
A
list of sequence databases, projects, and tools for C. elegans.
This is one page of the C. elegans WWW server which provides links
to other resources related to C. elegans research.
Caenorhabditis elegans Genome (NCBI)
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=celegans.inf
A complete
sequence of the Caenorhabditis elegans genome.
Caenorhabditis Genome Sequencing Projects (Sanger
Institute)
http://www.sanger.ac.uk/Projects/C_elegans/
Access
to sequences for C elegans and Cbriggisae;
site also provides analysis tools and links to other key resources.
Nematode Genome Resource (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/nematode/
A
collection of resources including links to genomic sequences in GenBank, and
other sequence information at NCBI. Also provides links to other major resource
and sequence data sites.
Nematode.net (Washington University’s Genome Sequencing Center
(GSC))
www.nematode.net
Nematode.net provides
information about several nematode genomes based on EST sequences. ESTs are available
for >30 nematodes other than Caenorhabditis
elegans---including key parasites of humans, animals, and plants. NemaGene
is composed of EST cluster consensus sequences for over 15 species, with functional
classification of sequences, and analysis/mapping of sequences based on InterPro
domains, KEGG pathways, and Gene Ontology classification. Nematode.net also
includes current information about the sequence status for all nematode species.
WormBase
http://www.wormbase.org/
WormBase is an international consortium working to provide access to current,
accurate, and curated information concerning the genetics, genomics, and biology
of C. elegans and related nematodes. The site contains a wide array
of data, including genomic sequences, gene information, cell lineages, microarray
data, and literature citations.
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Drosophila
BerkeleyDrosophila Genome Project (BDGP)
http://www.fruitfly.org/
A goal of the Drosophila Genome Project is to finish the sequence of the genome
of Drosophila to high quality with biological annotations. Access
to genomic sequence data is available along with tools to locate and analyze
genes and sequences. Other data from BDGC projects includes p-element gene
mutations, the sequence and expression of cDNAs, and SNP tables.
FlyBase
http://www.flybase.org/
FlyBase is a database of genetic and molecular data for Drosophila and
includes data on all species from the family Drosophilidae. FlyBase
includes information about genes and mutant alleles, the expression and properties
of transcripts and proteins, the functions of gene products, information about Drosophila genetic
and cytological maps. FlyBase also provides access to a bibliography of Drosophila citations
and genome data from major sequencing projects.
FlyMine ( University of Cambridge)
“An integrated database
for Drosophila and Anopheles genomics”
http://www.flymine.org/
The
FlyMine project is developing an open access, integrated database of genomic,
expression, and protein data for Drosophila and Anopheles to
support comparative genomics research. Many types of data are available, such
as genomes and genome annotation, gene expression and microarrays, various
types of deletions and mutations, and protein and proteomics.
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Escherichia coli
coliBASE
http://colibase.bham.ac.uk/
coliBASE brings together sequence data and tools for the comparative
genomics of E. coli and its relatives: Shigella and Salmonella.
The database contains the complete annotation of all genes from sequenced strains
and data from sequencing projects still in process. A whole genome viewer,
genome alignment tool, and other visualization tools are also provided.
EchoBase—an integrated post-genomic database for E. coli.
http://www.ecoli-york.org/
EchoBase, in addition to providing basic genome annotation, integrates information
from post-genomic experiments into a single resource. The goal of EchoBase
is to provide functional predictions for gene products whose functions are
not yet known. The database includes curated information (article summaries
and datasets) from a wide array of experiments including protein-protein interaction
studies, microarray data, functional genomics, and in silico bioinformatic
approaches.
EcoCyc (part of BioCyc)
http://EcoCyc.org/
EcoCyc database provides literature-based
curation of the entire genome and many metabolic and regulatory pathways
for the bacterium Escherichia coli K-12 MG1655. The goal of the
project is to cover all genes, proteins, and RNAs in the E. coli genome.
The database includes interactive diagrams and links to the literature and
to other databases such as RefSeq and Swiss-Prot.
EcoGene Database of Escherichia coli Sequence and Function
http://www.ecogene.org
EcoGene provides highly annotated E. coli sequences. Information
for all likely genes is organized into a searchable index of individual GenePages.
Each GenePage summarizes and provides links to sequence information, links
to other resources (such as Swiss-Prot and EcyCyc), genetic maps, and a bibliography
with links to Medline.
GenProtEC---E. coli Genome and Proteome Database
http://genprotec.mbl.edu
GenProtEC focuses on functions encoded by the Escherichia coli K-12
(strain MG1655) genome (GenBank Accession No. NC_000913.2) Annotations contain
multiple types of information, such as sequence similarities, classification
of gene products by structural domains, and cellular functions. Each gene record
also includes literature citations and links to related database entries.
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Medicago trunculata
Medicago truncatula Consortium
http://www.medicago.org/index.php
The Medicago truncatula Consortium’s
mission is to promote international and unrestricted data sharing from Medicago research
groups. The web site provides access to a variety of data and tools with the
goal of facilitating research in Medicago structural, comparative,
and functional genomics. This site provides access to the following databases
and projects, as well as researcher contacts, literature, and links.
- Genome Sequencing Project
http://www.medicago.org/genome/
This site coordinates and makes accessible genome sequence data from international
projects. Information also includes physical and genetic maps, molecular markers,
BAC sequences, genome browsers, annotation, and literature citations.
TIGR Medicago truncatula Database
http://www.tigr.org/tdb/e2k1/mta1/
The
database provides access to annotations generated at TIGR, and to Medicago ESTs
and BAC sequences from world-wide sequencing projects.
Also available is the
TIGR Medicago Gene Index: http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=medicago
UrMeLDB: The European Medicago Genome Database
http://mips.gsf.de/proj/plant/jsf/medi/index.jsp
Provides access to Medicago sequence data with an interactive genome
viewer and searchable tables of data with clones listed by chromosome, contigs,
and genetic elements. Genome annotation is performed by the International Medicago Genome
Annotation Group (IMGAG).
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Mouse
Mouse Genome Data (The Broad Institute)
http://www.broad.mit.edu/mouse/
Resources include links to the mouse genome sequences, genetic and physical
maps, and a mouse SNP database. The SNP database contains ~340,000 SNPs and
is being used to characterize mouse haplotypes. The Broad Institute is part
of the Mouse Genome Sequencing Consortium (which also includes Washington University
and the Sanger Institute).
Mouse Genome Informatics (MGI)
http://www.informatics.jax.org/
MGI
Database provides integrated access to extensive information on the genetics,
genomics, and biology of the laboratory mouse. Data, which are drawn from
several other projects, include information about genes and markers, gene
families, sequence data and maps, strains, polymorphisms, gene expression,
and comparative maps and data.
Mouse Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/mouse/
A guide to mouse genome resources at NCBI and other institutions. NCBI resources
include genome maps and sequence information for proteins and nucleotides,
SNPs, and comparative maps.
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Rat
Rat Mapping Resources (Wellcome Trust Centre for Human Genetics)
http://www.well.ox.ac.uk/rat_mapping_resources/
Website includes an integrated, interactive genetic linkage map of the rat
genome of 3 different rat pedigrees. Other information includes markers (SSLP,
microsatellites), congenics, and polymorphisms.
Rat Genome Database (RGD, Medical College of Wisconsin)
http://rgd.mcw.edu/
RGD is the result of collaboration between leading institutions involved in
rat genetic and genomic research. RGD functions as centralized repository of
rat genetic and genomic data. Mapping, strain, and physiological information
is also included. Another project goal is to provide curation of quantitative
trait loci, known mutations, and other phenotypic data. The site also provides
tools to search, mine, and analyze the data.
Rat (Rattus norvegicus) Genome Browser Gateway (UCSC)
http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=105195515&clade=vertebrate&org=Rat&db=0
Provides access to rat genome sequence information by several routes, including
searching or browsing chromosome maps. The Gene Sorter displays table of genes
that are related to one another in several possible ways, such as protein homology,
gene expression profiles, or genomic proximity.
Rat Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/rat/
A guide to rat genome resources at NCBI and other sites. NCBI resources include
genome maps and sequence information for proteins and nucleotides, SNPs, and
comparative maps.
RatMap—Rat Genome Database
http://www.ratmap.org/
RatMap provides information about rat genes, including nomenclature, chromosomal
position and markers, gene function, links to other resources (GenBank, UniGene),
and literature references. RatMap also supports comparative mapping with several
species: bovine, human, and mouse.
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Saccharomyces
Comprehensive Yeast Genome Database (CYGD; MIPS)
http://mips.gsf.de/genre/proj/yeast/
CYGD
provides extensive information about the molecular structure and functional network
of the yeast genome, plus data from related yeasts for comparative research.
Genomic data includes an interactive graphical genome viewer with summary tables
for the entire genome or for individual chromosomes (nuclear or mitochondrial).
The genome is annotated with respect to genetic, biochemical, and cellular function.
Additional protein and functional information include protein interactions, protein
complexes, and functional families. Much of CYGD’s
information is manually extracted and annotated from the yeast literature,
including experimental data from functional analysis projects. The database
is cross-references to other databases (NCBI, PIR, PEDANT, EMBL) to provide
complementary material.
Saccharomyces Genome Database (SGD; Stanford University)
http://www.yeastgenome.org/
SGD collects information and maintains a curated database of the molecular
biology of Saccharomyces cerevisiae. SGD contains the full sequence
of the Saccharomyces genome along with a variety of tools, display options,
and other resources. Some of these features are:
- Global Gene Hunter which retrieves information for a given locus from seven
major databases: SGD, Genbank, PubMed, PDB Homolog, Swiss-Prot, Comprehensive
Yeast Genome Database (MIPS), and Protein Information Resource (PIR).
- Table of Gene Summary Paragraphs lists genes that have a written synopsis
of published information, and includes selected references.
- The Protein Page summarizes basic protein information calculated from the
predicted sequence, with links to structure resources.
- Function Junction retrieves functional analyses data for a locus from six
major project sites, including: SGD SAGE Query, Yeast Microarray Global Viewer,
and Yeast Protein Function Assignment.
Additional information resources include: an interactive genome viewer, gene
expression and microarray data from published research, and information about
biochemical reactions.
Yeast Comparative Genomics (Broad Institute, MIT)
http://www.broad.mit.edu/annotation/fungi/comp_yeasts/
Sequence information and the results of comparative analyses for three yeast
species in addition to S. cereviae: S. paradoxus, S. mikatae, and S.
bayanus. Data is available to download or searching. Multiple alignments
and motif searching are also available for species comparisons.
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Xenopus
Xenopus Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/frog/
A summary of resources related to Xenopus genome and biology.
Includes direct links to NCBI map, sequence, and taxonomy data and to other
sequencing projects and web sites.
Xenbase: a Xenopus web resource
http://www.xenbase.org/
Collection of links to information and resources for X. laevis and X.
tropicalis. Includes genomic information, EST collections, microarrays,
literature citations, and more.
The Xenopus tropicalis EST Project (Sanger Institute and Wellcome
Cancer Research)
http://www.sanger.ac.uk/Projects/X_tropicalis/
A collection of about 55,000 ESTs are available for BLAST searching
or downloads. Return to Top
Zebrafish
The Danio rerio Sequencing Project (Sanger Institute)
http://www.sanger.ac.uk/Projects/D_rerio/
Zebrafish genome maps and sequence data available (about two thirds of the
total genome has been sequenced). Also includes microarray and mutation data.
Links to zebrafish resources at Ensembl.
Zebrafish Gene Index (ZGI)
http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=zfish
ZGI
integrates research data from zebrafish (Danio rerio) gene research projects
with the goal of presenting a non-redundant view of all zebrafish genes with
data on expression patterns, functions, and evolutionary relationships.
Zebrafish Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/zebrafish/
A guide to zebrafish genome resources at NCBI and other sites. NCBI resources
include genome maps and sequence information for proteins and nucleotides.
The Zebrafish Information Network
http://zfin.org
ZFIN’s goals include
production of the community database and resource for zebrafish research, the
development of integrated genetic, genomic,and developmental information, and
the provision of links to data in other model organism and human databases. ZFIN
serves as a central access point for zebrafish information and analytic tools.
Genome information includes sequences, annotations, and gene predictions (and
ESTs) from major projects and databases (Sanger, Ensembl, Vega, UCSC). Protein
information includes feature and domain annotations. Maps, genes, and comparative
analysis are also included.
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More tools and sources for Model Organisms
UBC: Bioinformatics Links Directory: Model Organisms
http://bioinformatics.ca/links_directory/?category_id=5
A
large collection of links to resources--databases and tools--for a wide variety
of model organisms.
Model Organisms Guide (NCBI)
http://www.ncbi.nlm.nih.gov/About/model/mammal.html
Describes a variety of model organisms and provides links to NCBI resource
pages where available, or directly to sequence information for the organisms
(major model organisms) or groups (e.g. archaea, retroviruses).
Model Organisms for Biomedical Research (NIH)
http://www.nih.gov/science/models/
Central page provides information about national and international activities
and major resources for biomedical research using several model organisms.
Links to information pages for these species: Arabidopsis, mouse,
rat, yeast, Neurospora, Dictyostelium, C. elegans, Drosophila, zebrafish,
and Xenopus.
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