What is a RefSeq record?
RefSeq genomes are copies of selected assembled genomes available in GenBank. RefSeq transcript and protein records are generated by several processes including: Computation. Eukaryotic Genome Annotation Pipeline. Prokaryotic Genome Annotation Pipeline.
What is RefSeq status?
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products.
How many human gene sequence entries are there in NCBI RefSeq?
RefSeq FTP release 71 (July 2015) includes more than 77 million sequence records for more than 55 000 organisms….
| Release Directory | Bacteria |
|---|---|
| Organisms | 39660 |
| % Change | 40 |
| Transcripts | 19650 |
| % Change | 488 |
What are RefSeq identifiers?
The RefSeq ID is a unique identifier given to a sequence in the NCBI RefSeq database. The RefSeq database is a curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, and entire chromosomes. These variables are used to make the Web link to the RefSeq database.
What is the difference between GenBank and RefSeq?
What is the difference between RefSeq and GenBank? GenBank sequence records are owned by the original submitter and cannot be altered by a third party. RefSeq sequences are not part of the INSDC but are derived from INSDC sequences to provide non-redundant curated data representing our current knowledge of known genes.
What kind of database is RefSeq?
INTRODUCTION. RefSeq is a public database of nucleotide and protein sequences with corresponding feature and bibliographic annotation. The RefSeq database is built and distributed by the NCBI, a division of the National Library of Medicine located at the US National Institutes of Health.
Why are there 3 possible reading frames?
During transcription, the RNA polymerase read the template DNA strand in the 3′→5′ direction, but the mRNA is formed in the 5′ to 3′ direction. The mRNA is single-stranded and therefore only contains three possible reading frames, of which only one is translated.
Is RefSeq a primary database?
The RefSeq collection is derived from the primary submissions available in GenBank. GenBank is a redundant archival database that represents sequence information generated at different times, and may represent several alternate views of the protein, names or other information.
What is the difference between GenBank and RefSeq database?
Why does DNA have 6 reading frames?
MLA CE Course Manual: Molecular Biology Information Resources (Genetics Review: Reading Frames) A reading frame refers to one of three possible ways of reading a nucleotide sequence.
What way is DNA read?
DNA is ‘read’ in a specific direction, just like letters and words in the English language are read from left to right. Each end of DNA molecule has a number. One end is referred to as 5′ (five prime) and the other end is referred to as 3′ (three prime).
How many genomes are in the RefSeq?
Abstract. The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation.
How are RefSeq records derived from sequence data?
RefSeq records are derived from publicly available sequence data; varying levels of validation, additional annotation, and manual curation are applied to the RefSeq record. NCBI Reference Sequences are provided through the separate processes described below.
Where can I find RefSeq Records in NCBI?
RefSeq records can be retrieved by querying with an accession number, symbol or locus_tag, name, or by using Entrez Limits and Property terms. RefSeq records can be accessed through several NCBI resources including BLAST, Entrez (Nucleotide, Protein, Gene, Protein Clusters, BioSystems), Genome Data Viewer, and FTP as follows:
What does the comment section in a RefSeq record mean?
Comment:RefSeq records contain a COMMENT section that includes the term REFSEQ and identifies the record status, the source accession(s) used to derive the RefSeq sequence (if applicable), and the collaborating group, if any. Nomenclature:RefSeq records consistently use official nomenclature for the gene feature, when available.
Who is responsible for curation of RefSeq Records?
RefSeq transcript and protein records for a subset of organisms, primarily mammals, are curated by NCBI staff. Curation is an ongoing process and some records have not been reviewed yet; the curation status is indicated on the RefSeq record in the COMMENT block.