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TAIR integrates information about the Arabidopsis genome, genes, gene products, natural variants, mutant alleles and plant phenotypes and research literature. Data in TAIR can be retrieved using simple and advanced searches, bulk query and download tools, and in collections of prepared text files.
Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non-coding sequences: Fungi, Prokaryotes, Metazoa, Protist, Plants [41] [42] PHANOTATE: A tool to annotate phage genomes. Phages [43] SplicePredictor
Tools for querying and downloading gene expression profiles are provided. Human Protein Atlas (HPA [10]): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. Legume Information System (LIS): genomic database for the legume family [11]
As of 2002, the number of classified green plant species was estimated to be around 370,000, however, there are probably many thousands more yet unclassified. [10] Despite this number, very few of these species have detailed DNA sequence information to date; 125,426 species in GenBank, as of 11 April 2012, [11] but most (>95%) having DNA sequence for only one or two genes. "...almost none of ...
For each model organism, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. RefSeq is limited to major organisms for which sufficient data are available (121,461 distinct "named" organisms as of July 2022), [ 4 ] while GenBank includes sequences for any ...
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 ...
Gramene [17] is an online web database resource for plant comparative genomics and pathway analysis based on Ensembl technology. Plant Genome DataBase Japan [18] (PGDBj) is a website that contains information related to genomes of model and crop plants from databases. It has three main components: ortholog db, DNA marker and linkage map db, and ...
TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S.cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members. TreeFam is also an ortholog database.