What is the difference between accession number and RefSeq?
What is the difference between accession number and RefSeq?
RefSeq records are distinguished from INSDC records by: Accession format: The most distinguishing feature of a RefSeq record is the distinct accession number format that begins with two characters followed by an underscore (e.g., NP_). INSDC accession numbers never include an underscore.
Is GENCODE the same as Ensembl?
In practical terms, the GENCODE annotation is essentially identical to the Ensembl annotation.
What is the difference between RefSeq and Gen bank?
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 does GENCODE stand for?
GENCODE
| Acronym | Definition |
|---|---|
| GENCODE | Generalized Coding (Graphics Communications Association) |
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.
What Gencode produces?
The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.
What is XP in NCBI?
The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies.
What GENCODE produces?
What does NC mean in NCBI?
reference assembly
From The NCBI Handbook, ch18: (via this answer) NC – “Complete genomic molecule, usually reference assembly”
Which is more comprehensive, GENCODE or RefSeq?
Gencode is in almost all cases more comprehensive. For example, this is NCBI RefSeq vs Ensembl (v24, release 83) for BRCA gene: RefSeq and Gencode are not interchangeable in most cases, though RefSeq annotations will often be a subset of the Gencode ones. How is the BRCA screenshot making your point?
Where can I find the RefSeq gene set?
The widely used RefSeq geneset is produced by NCBI [ 15 ]. It can also be visualised using the UCSC and Ensembl browsers, and downloaded from http://www.ncbi.nlm.nih.gov/RefSeq. The RefSeq human protein-coding transcript set also contains a significant manually annotated component.
What is the difference between a GenBank ( GCA ) and RefSeq?
What is the difference between a GenBank (GCA) and RefSeq (GCF) genome assembly? A GenBank (GCA) genome assembly contains assembled genome sequences submitted by investigators or sequencing centers to GenBank or another member of the International Nucleotide Sequence Database Collaboration (INSDC).
Are there any gene annotations more complete than RefSeq?
They found that the human gene annotations in the three databases are far from complete, although Ensembl and AceView annotate many more genes than RefSeq. In this paper, we performed a comprehensive evaluation of different annotations on RNA-Seq data analysis, including RefGene, UCSC, and Ensembl.