The TIGR Databases are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
Phytophthora comprise a group of plant pathogenic organisms (Oomycetes) that attack an extremely broad range of agronomically important species, affecting many major crops worldwide. Their cumulative global damage is estimated at billions of dollars annually.
SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
The Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae.
Established in 1996 as part of the BBSRC's Plant and Animal Genome Analysis special initiative, our focus is the development, management and distribution of information relating to comparative mapping and genome research in crop plants.
AGR is a database developed at NASC using the ACEDB database system. Sequences, maps, and other information has been combined to form a large and powerful information resource.
The overall goal of the Mouse Genome Sequence (MGS) project is to integrate emerging mouse genomic sequence data with the genetic and biological data available in MGD and GXD. MGS is part of the informatics infrastructure needed to support mouse-human comparative genomics.
To cross-reference homologous genes in yeast and human, all yeast ORF protein sequences from the Saccharomyces Genome Database (SGD) were used as queries against a six-frame translation of the human EST subset of the Database of Expressed Sequence Tags (dbEST).
LocusLink provides link to curated sequence and descriptive information about genetic loci. Information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and related web sites.
SRPDB (Signal Recognition Particle Database) Provides Aligned, Annotated and Phylogenetically Ordered Sequences Related to Structure and Function of SRP.
The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
Sequence collection, deprived from redundancy, of 5' and 3' UTR sequences from eukaryotic mRNA, collection of functional sequence patterns located in 5' or 3' UTR sequences.
SMART, a simple modular architecture research tool: identification of signaling domains. Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known.
PDB, the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
IMB Jena Image Library of Biological Macromolecules, access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).
ASTRAL compendium provides databases and tools for analyzing protein structures and sequences, partially derived from, and augments the SCOP: Structural Classification of Proteins database.
The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
searching algorithm SYSTERS (SYSTEmatic Re-Searching) is based on iterative calls of a traditional database search tool like BLASTP or FASTA. The searching algorithm explores the sequence space around a query sequence - called seed - and finds a set of related sequences to this seed - called cluster - which share a strong similarity.
The ProClass database is a non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
Thermodynamic Database for Proteins and Mutants (ProTherm) contains numerical data of several thermodynamic parameters, namely, Gibbs free energy, enthalpy, heat capacity, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins upon mutations.
The Danish Centre for Human Genome Research's 2-D PAGE Databases are being developed for functional genome analysis in health and disease. They contain data on proteins identified on various reference maps. You can display protein names and information on specific protein spots by clicking on the image. You can search by protein name, keywords, Mr and pI or organelle or cellular component. Protein files contain extensive links to other databases (MEDLINE, GenBank, Swiss-Prot, PIR, PDB, OMIM, UniGene, GeneCards, etc.) or Web sites.
The DataBase contains data from several Mycobacteria strains, Helicobacter pylori, Borrelia garinii and Jurkat T cells. The DB complies with the rules of the world-2D-database and is linked to several sequence databases.
Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site.
TransTerm is a database of sequence contexts about the stop and start codons of many species found in GenBank. TransTerm also contains codon usage data for these same species and summary statistics for the sequences analysed. The 3' and 5' UTR flanking sequences and coding sequences for each organism are also available for searching via our experimental server. We have also have a great deal of other information 'in house' that we have not yet been able to make easily available. Contact the authors if you would like this information before it is available through this interface.
The Alternative Splicing DB (ASDB) has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns.
TRRD is designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes. The TRRD format allows to describe the modular structure of transcription regulatory regions and the hierarchy of theirs constituent regulatory units.
EPD - The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression) is a web site dedicated to methodologies, tools, and technologies relating to information in the study of gene expression.
MEROPS database provides a wealth of information on proteases. There is a page describing each individual protease as well as one for each of the families into which they can be grouped, and even for each of the clans into which the families can be grouped. Many hundreds of proteases can be found by name, identifier or the organism in which they occur.
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
This database is an attempt to gather information about the DExH/D protein family with particular emphasis on the biochemical and functional characteristics of these proteins. Because DExH/D proteins are essential in numerous fundamental biological processes, research concernig these proteins is conducted in various disciplines such as biochemistry, genetics and biophysics.
Intein Database - Protein splicing is defined as the excision of an intervening protein sequence (the INTEIN) from a protein precursor and the concomitant ligation of the flanking protein fragments (the EXTEINS) to form a mature extein protein and the free intein.
The ABI Genetic Linkage Panels are being typed in ten worldwide populations by the Kidd Lab, Department of Genetics, Yale University School of Medicine. We will post allele frequencies in this site as soon as they become available. However, it must be noted that these allele frequencies should be used for reference purposes only. Authors wishing to perform statistical analyses on these data should contact Kenneth K. Kidd first.
KEYNET is a database of Keywords extracted from EMBL and GenBank databases. The Keynet structure is based on biological criteria aimed to assist the user in data searching and to minimize the risk of loss of information.
Minnesota Biocatalysis/Biodegradation Database Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds.
