How many protein sequences are in the non-redundant NCBI database?
The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins (RefSeq release 19).
What is a non-redundant protein database?
in public databases, a Non-Redundant (NR) database was introduced by the National Center for Biotechnology Information (NCBI) . NR is defined by NCBI as protein sequences that have 100% identity and are the same protein length.
What is NR database NCBI?
The nr database is compiled by the NCBI (National Center for Biotechnology Information) as a protein database for Blast searches. It contains non-identical sequences from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF. The strengths of nr are that it is comprehensive and frequently updated.
What is non-redundant database in blast?
Non-redundant: manual curation used to provide only one entry per protein product; variants are annotated in entry. Highly-cross-referenced to other databases.
How many sequences are in an NR database?
Since July 2021, NCBIprot contains at least 409 million sequences.
How big is the NR database from NCBI?
The protein nr database contains about 54 billion residues, so the sequences require 51 GB. The total size of the nt database as of this writing (03/15/2018) is 54 GB and the size of nr is 154 GB.
What is the meaning of non-redundant?
: not characterized by repetition or redundancy : not redundant nonredundant functions nonredundant rules.
What are redundant proteins?
A redundant proteome is one in which all or nearly all protein sequences are highly similar or identical to an existing proteome from the same species.
What is the non-redundant database in NCBI?
Based on NCBI’s own definition, “RefSeq database is a non-redundant set of reference standards derived from the INSDC databases that includes chromosomes, complete genomic molecules (organelle genomes, viruses, plasmids), intermediate assembled genomic contigs, curated genomic regions, mRNAs, RNAs, and proteins.
What is NR and NT?
In that case, “nr/nt” stands for “non-redundant nucleotide.” However, as you point out, NCBI also make separate databases available for download. In this case, “nr” is non-redundant protein, “nt” is non-redundant nucleotide.
What is data redundancy in a database?
Data redundancy occurs when the same piece of data exists in multiple places, whereas data inconsistency is when the same data exists in different formats in multiple tables.
How big is the nr database?
Is the NCBI Reference Sequence database redundant or non redundant?
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins.
When does NCBI annotate a non redundant protein?
When the NCBI genome annotation pipeline annotates a bacterial protein that is 100% identical and the same length as an existing non-redundant protein, NCBI will annotate that protein on the genome by referencing the WP_ accession in the annotated CDS feature.
When to use a single source feature for a non redundant protein?
A single source feature is provided when the non-redundant protein is found on genomes within a single super-kingdom (e.g., WP_003547430.1 or WP_000091939.1) The organism and NCBI tax_id indicated reflect the lowest common level, for the set of genomes that the protein is annotated on.
Where are non redundant proteins found in a RefSeq genome?
Because a non-redundant protein sequence may be found in RefSeq genomes from multiple species, the organism information provided on the protein record reflects the lowest-common taxonomic node ranging from the genus species level to super-kingdom.