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Checks for a start or stop codon in the reference genome sequence Internal stop: Checks for the presence of an internal stop codon in the genomic sequence NCBI:Ensembl protein length different: Checks if the protein encoded by the NCBI RefSeq is the same length as the EBI/WTSI protein NCBI:Ensembl low percent identity
LRG records are recommended in the Human Genome Variation Society Nomenclature guidelines as reference sequences to report sequence variants in LSDBs and the literature. The LRG concept was developed by the GEN2PHEN project in conjunction with the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI).
UCSC Malaria Genome Browser: genome of malaria causing species (Plasmodium falciparum and others) Wormbase: genome of the model organism Caenorhabditis elegans and WormBase ParaSite for parasitic species; Xenbase: genome of the model organism Xenopus tropicalis and Xenopus laevis; Zebrafish Information Network: genome of this fish model organism
The National Center for Biotechnology Information (NCBI) [1] [2] is part of the (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
Several projects to improve RefSeq services are currently in development by the NCBI, often in collaboration with research centers such as EMBL-EBI: . Consensus CDS (CCDS): This project aims to identify a core set of human and mouse protein-coding regions and standardize sets of genes with high and consistent levels of genomic annotation quality.
The dbSNP accepts apparently neutral polymorphisms, polymorphisms corresponding to known phenotypes, and regions of no variation. It was created in September 1998 to supplement GenBank, NCBI’s collection of publicly available nucleic acid and protein sequences. [2] In 2017, NCBI stopped support for all non-human organisms in dbSNP. [3]
NCBI COGs: resources of phylogenetic studies of proteins encoded in complete genomes. GLAMM: the Genome-Linked Application for Metabolic Maps, which is an interactive viewer for metabolic pathways and experiments. GLAMM Tutorial: a comprehensive guidance for using GLAMM. MEGABLAST Search: NCBI's introduction to the MEGABLAST algorithm.
Locus Reference Genomic (LRG) records have unique accession numbers starting with LRG_ followed by a number. They are recommended in the Human Genome Variation Society Nomenclature guidelines as stable genomic reference sequences to report sequence variants in LSDBs and the literature.