Bioinformatics & Genomics
Genomics & DNA Sequence Analysis
DNA Sequence Analysis
DNA Sequencing Software
Genomic Search Servers
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[USDA/ARS] A developing database of the alfalfa genome.
ARS Genome Database Resource
[USDA-ARS Center for Agricultural Bioinformatics, Cornell University ] A site with plant genome databases and information. Included are plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varities that possess query traits.
Artemis sequence viewer
[The Sanger Centre, U. K.] The Artemis sequence viewer and annotation tool allows visualization of DNA sequence features and sequence analysis, including six-frame translation. Artemis can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Written in Java, Artemis is available for UNIX, Macintosh or MS Windows.
Berkeley Drosophila Genome Project
[Univ. of California, Berkeley] (BDGP) A comprehensive site with information on the fruit fly and its genome-related projects, and links to gene and genome analysis tools.
Berkeley Sequence and Structure Search Site
[University of California, Berkeley] Computational biology site dedicated to aiding biomolecular sequence and structure searching. Along with selected database-searching resources, site offers advice for sequence searching.
[SRI International] The BioCyc Knowledge Library is the new name for EcoCyc and MetaCyc. It is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
[Osaka University] A human and mouse gene expression data bank, collecting quantitative and qualitative information on gene expression.
Canadian Bioinformatics Resource
[National Research Council Canada] Canadian Bioinformatics Resource is dedicated to providing the Canadian research community with convenient, effective
access to widely used bioinformatics tools and databases.
CGSC: E. coli Genetic Stock Center
[Yale University] A database of genetic information, including genotypes and reference information for the strains in the CGSC collection, gene names, properties, linkage map, gene product information, and information on specific mutations.
[Kazusa DNA Research Institute] The genome database for Synechocystis sp. strain PCC6803.
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dbEST: Expressed Sequence Tags database
[The National Center for Biotechnology Information] dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
[National Center for Biotechnology Information] A public database of genome survey sequences including contact information about the contributors, experimental conditions, and genetic map locations.
[National Center for Biotechnology Information] A public database that contains sequence and mapping data on short genomic landmark sequences or sequence tagged sites.
DDBJ: DNA Data Bank of Japan
The international DNA database, which shares data with the NCBI and EBI DNA databases.
Deinococcus radiodurans Genome Search
[TIGR] Users can view the predicted coding regions found within a span of the Deinococcus radiodurans chromosome.
DNA vs Protein
[The Sanger Centre] Compares a protein sequence or a protein profile-HMM to genomic DNA. It uses the 'GeneWise' class of algorithms to provide a combined homology and gene prediction alignment of the protein to the DNA sequence.
ECDC: E. coli Database Collection
[Univ. of Giessen] A site dedicated to the E. coli K-12 chromosome.
EGAD: Expressed Gene Anatomy Database
[The Institute for Genomic Research] A collection of human transcript sequences from extracting and curating sequences from GenBank, creating a non-redundant set of human transcript (HT) sequences.
EMBL Nucleotide Sequence Database
[European Bioinformatics Institute] A database of DNA and RNA sequences collected from the scientific literature and patent applications and directly submitted from researchers and sequencing groups. Data are shared with the DDBJ and NCBI.
[EMBL, EBI, Sanger Institute] (Human Genome Server) Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
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[National Center for Biotechnology Information] Performs a nucleotide sequence search retrieving molecular biology data and bibliographic citations from the NCBI's integrated databases.
[Indiana Univ.] A database of the Drosophila genome.
GDB: The Genome Database
[Johns Hopkins Univ.] A international collaboration on the Human Genome Project.
[National Center for Biotechnology Information] The major database in the US of DNA sequences compiled by scientists world-wide.
Gene Map of the Human Genome
[National Center for Biotechnology Information] Chromosome maps of the human genome.
[Weizmann Institute of Science ] GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
GeneCensus Genome Comparisons
[Yale University] This site provides genome and phylogenetics related information, databases, and services for many classes of organisms, mainly microscopic.
Genome Database (Saccharomyces)
[Stanford Univ.] A searchable database of the molecular biology and genetics of baker's yeast.
Genome Project (E. coli)
[University of Wisconsin - Madison] Contains the completed sequence of the E. coli K-12 genome and several of the phages. Currently in the process of analyzing the data acquired.
Genome Project (Mycoplasma pneumoniae)
[Zentrum fur Molekulare Biologie der Universitat Heiderlberg] DNA sequence of the complete Mycoplasma pneumoniae genome.
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Genome Sequencing Center Jena
[Institute of Molecular Biotechnology] The purpose of the Genome Sequencing Center is to further the knowledge of genomes, particularly
the human genome, through large scale sequencing and genetic
analysis. Data from human, mouse, Dictyostelium (amoeba), and bacterial genomes are available.
[CBS] This site provides DNA structural analysis of complete genomes and chromosomes.
[GEN Research Institute & Human Genome Center] A human cDNA database achieved through a large-scale human cDNA analysis project containing sequence information and data concerning chromosomal localizations and expression patterns.
[The Organelle Genome Database] A taxonomically broad organelle genome database that organizes and integrates diverse data related to organelles.
HIDB: Haemophilus influenzae Rd Genome Database
[The Institute for Genomic Research] The latest sequence data and related annotation for the Haemophilus influenzae Rd genome.
HIV Sequence Database
[Los Alamos National Lab] This database currently contains nucleotide sequences that have appeared in the current and all previous annual editions of Human Retroviruses and AIDS in both GenBank and EMBL formats, as well as protein translations of the coding regions.
HPV Sequence Database
[Los Alamos National Laboratory] The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins.
[InfoBiogen] HuGeMap is a database that contains the genetic maps from Généthon and Cooperative Human Linkage Center, and the physical maps from CEPH/Généthon and the Whitehead Institute-MIT.
Influenza Sequence Database
[Los Alamos National Laboratory] A curated database of nucleotide and amino acid sequences intended to provide an easy sequence deposit and retrieval capabilities to the analysis of hemagglutinin and neuraminidase sequences.
Integrated X Chromosome Database
[Max-Planck-Institute for Molecular Genetics] Includes DNA classes, clones, genes, STS, EST, probes, cDNA, chromoband, and collections for X chromosome sequencing.
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[Univ. of Missouri-Columbia] Provides a public Internet gateway to the current knowledge of the maize genome and its expression.
MGDB: Mycoplasma genitalium Genome Database
[TIGR] The first genome of a gram positive-like bacterium to be completed.
[EMBL-EBI] Provides a comprehensive and integrated DNA database on mitochondrial genes both from different organisms (humans, animals, plants and microbes) and from intraspecies variants and mutants.
[Center for Molecular Medicine, Emory Univ. School of Medicine] A human mitochondrial genome database.
MJDB: Methanococcus jannaschii Genome Database
[The Institute for Genomic Research] The latest sequence data and related annotation for the genome.
Mosquito Genomics WWW Server
[Colorado State University] Provides access to mosquito genomics databases, both cross species and species specific.
[Zebrafish Information Network] Developing database covering various types of data such as mutations, gene expression patterns, and the genetic map.
NRSub: Non-Redundant B. subtilis database
[Pole Bio-Informatique Lyonnais] A database of sequences and information on the completed Bacillus subtilis genome.
[Munich Information Center for Protein Sequences] (Protein Extraction, Description, and ANalysis Tool) "PEDANT is a software system for completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes."
Plant Genome Data & Information Center
[USDA National Agricultural Library] This USDA site provides access to a variety of information products and services that relate to many aspects of plant and animal biotechnology and genomics.
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[Lundberg Laboratory] Rat genome database that allows sequence searches as well as viewing of linkage/physical maps and homology tables.
WormBase (Caenorhabditis elegans)
[CalTech, CSHL, WUSTL, The Sanger Center, and Le Centre National de la Recherche Scientifique of Fran] This is a repository of mapping, sequencing, and phenotypic information about the C. elegans nematode.