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The apple genome has approximately 57,000 genes, which was the highest number of any plant genome studied at the time, and more genes than the human genome which has about 25,000 genes. The modern apple has 17 chromosomes which were found to be derived from an ancestor with 9 chromosomes that experienced genome-wide duplication.
Efficient querying of genomic reference databases including UniProt, National Center for Biotechnology Information, and Ensembl genome database project: Linux, macOS, Windows: BSD: Laura Luebbert and Lior Pachter: GROMACS: Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. Linux, macOS, Windows ...
RGD (Rat Genome Database): genomic and phenotype data for Rattus norvegicus; Saccharomyces Genome Database: [12] genome of the yeast model organism; SNPedia; SoyBase Database [13] (SoyBase): USDA soybean genetics and genomic database ; UCSC Malaria Genome Browser: genome of malaria causing species (Plasmodium falciparum and others)
The BioCyc database collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to genome and metabolic pathway information for thousands of organisms. [1] As of July 2023, there were over 20,040 databases within BioCyc. [2]
Saccharomyces cerevisiae was the first eukaryotic organism to have its complete genome sequence determined.. This list of "sequenced" eukaryotic genomes contains all the eukaryotes known to have publicly available complete nuclear and organelle genome sequences that have been sequenced, assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences.
Chado makes extensive use of controlled vocabularies to type all entities in the database; for example: genes, transcripts, exons, transposable elements, etc., are stored in a feature table, with the type provided by Sequence Ontology. When a new type is added to the Sequence Ontology, the feature table requires no modification, only an update ...
Since 2011, the GOLD database has been run by the DOE Joint Genome Institute. The GOLD database was created in 1997; the first version of the database contained information for 350 sequencing projects, of which 48 had been completely sequenced with their analyses published. [1] GOLD v.5 was released on 28 May 2014.
Genome sequence annotations Location of genes and regulatory regions in the genome; Functional curation of gene products Discern functions fulfilled by the gene product by looking at a variety of data including Gene Ontology (GO) annotations, phenotypes, gene expression, pathway information; Protein/RNA sequence annotations; Anatomical information