Biology: Genome databases

High quality (6.5X) draft sequence from a female North American green anole lizard - As the first reptile genome sequenced, the anole genome is taxonomically far from other sequence and annotated genomes and very few ESTs or cDNA are available for this species. Thus, a number of EST sequences were produced for an initial gene annotation. Illumina-based RNA-seq to improve the Anolis annotation is currently underway.

User-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) reseacher in mind, but a couple of them can be useful to the wider research community. Site created by the University of Toronto Centre for the Analysis of Genome Evolution & Function.

from York University Libraries

Genomic sequence data and manually curated functional information about genes and proteins of the human fungal pathogen Candida albicans and related species.

Results from collaborative undergraduate student research on determining coding sequence, localization, and expression patterns for various Tetrahymena genes by searching the Gene Database. Progress on gene knockout constructions are also available.

Genomes for Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium fasciculatum, Polysphondylium pallidum

TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from scientific literature, the research community, and many other sources.

TetraFGD provides RNA-seq, MICROARRAY, GENE NETWORK and PHOSPHOPROTEOME data for T. thermophila using Gene ID or Gene description searches or Blast Sequences

Database of Drosophila Genes and Genomes

IchDB is a user-updatable database of information about the Ichthyophthirius multifiliis genome sequence determined at The J. Craig Venter Institute (JCVI). IchDB provides information on the genome, genes, and proteins of Ichthyophthirius collected from scientific literature, the research community, and many other sources.

USDA/ARS funded database focused on the crop plant and model organism Zea mays.

Integrated genetic, genomic, and biological data of the laboratory mouse to facilitate the study of human health and disease

OxyDB is a user-updatable database of information about the Oxytricha trifallax genome sequence, determined at the Washington University Genome Sequencing Center. OxyDB provides information on the genome, genes, and proteins of Oxytricha based on analyses performed at Princeton University, scientific literature published by the Oxytricha research community, and other sources.

Scientific data for the fission yeast Schizosaccharomyces pombe including genomic sequence and features, genome-wide datasets and manual literature curation.

PortEco is a next-generation resource for knowledge and data about the biology of Escherichia coli K-12 group strains, its bacteriophages, plasmids, and mobile genetic elements. PortEco is being developed by a national consortium of both laboratory biologists and computational biologists, and is funded by a grant from the U.S. National Institutes of Health.

Comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data

TAIR maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive links to other Arabidopsis resources.

Genetics, genomics and biology of C. elegans and related nematodes

Community database resource for the laboratory use of zebrafish. Includes integrated zebrafish genetic, genomic and developmental information, reference data sets of zebrafish research information, links to corresponding data in other model organism and human databases.

Diverse and rich genomic, expression, and functional data from Xenopus research.

Summary of Arabidopsis thaliana, Strain col, version 19.0. Includes database search and analysis tools.

BsubCyc is a model-organism database for the bacterium Bacillus subtilis, based on the updated B. subtilis 168 genome sequence and annotation published by Barbe et al. in 2009. Tools provided include a genome browser, display of individual metabolic pathways and of full metabolic maps, multiple analysis methods for user-supplied omics and multi-omics datasets, storing groups of genes and pathways in your account, and comparative analysis tools.

The EcoCyc project performs literature-based curation of the entire genome of the bacterium Escherichia coli K-12 MG1655, and of transcriptional regulation, transporters, and metabolic pathways. Database tools include a genome browser, individual metabolic pathways and full metabolic maps, analysis methods for user-supplied omics and multi-omics datasets, storing and analyzing groups of genes and pathways in your account, and comparative analysis tools.

Encyclopedic reference on human metabolic pathways including a zoomable human metabolic map diagram and tools for querying, visualizing, and analyzing the underlying database, and for analyzing omics data such as multiple pathway-analysis methods for omics and multi-omics datasets, storing groups of genes and pathways in your account, and Metabolism → Matabolic Route Search.

Summary of Leishmania major, Strain strain Friedlin, version 19.0. Includes database search and analysis tools.

MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. MetaCyc aims to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.

Summary of Trypanosoma brucei, version 19.0. Includes database search and analysis tools.

Genomic, metabolic pathway, reaction, enzyme, and compound information manually curated from the scientific literature

Links to 5500 databases within the BioCyc collection. Tier 1 Pathway/Genome databases have received at least one year of literature-based curation by scientists. Tier 2 databases were generated by the PathoLogic program which was used to predict metabolic pathways, operons (for bacteria only), and their pathway hole fillers (for many of the PGDBs). The resulting PGDBs underwent manual review by a person to remove false-positive pathway predictions that they could detect and to perform other manual polishing steps such as defining protein complexes as well as less than one year of literature-based curation. Most Tier 2 PGDBs have undergone 1-4 months of curation.

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.

The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies (Wu et al., 2003).

The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

Includes databases such as PubMed, GenBank (genetic sequence database), Gene Expression Omnibus Database, Protein database

ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

BLASTP programs search protein databases using a protein query.