RefSeq

A propos

RefSeq est la base de données NCBI de séquences de référence ; un ensemble organisé et non redondant comprenant des contigs d'ADN génomique, des ARNm et des protéines pour des gènes connus, ainsi que des chromosomes entiers.

Accession numbers et types de molécules

Les entrées RefSeq sont similaires au format d'entrée de GenBank. Attribuer une nouvelle entrée RefSeq inclus un unique préfixe d'accession suivi d'un underscore. Le préfixe d'accession RefSeq a une signification implicite en termes de type de molécule qu'il représente. Voici tous les préfixes d'accession RefSeq et le type de molécule associé provenant de la Table 1 du
Chapitre 18 The Reference Sequence (RefSeq) Database retrouvé dans The NCBI Handbook

Accession prefix	Molecule type	Comment
AC_	Genomic	Complete genomic molecule, usually alternate assembly
NC_	Genomic	Complete genomic molecule, usually reference assembly
NG_	Genomic	Incomplete genomic region
NT_	Genomic	Contig or scaffold, clone-based or WGSa
NW_	Genomic	Contig or scaffold, primarily WGSa
NZ_	Genomic	Complete genomes and unfinished WGS data
NM_	mRNA	Protein-coding transcripts (usually curated)
NR_	RNA	Non-protein-coding transcripts
XM_	mRNA	Predicted model protein-coding transcript
XR_	RNA	Predicted model non-protein-coding transcript
AP_	Protein	Annotated on AC_ alternate assembly
NP_	Protein	Associated with an NM_ or NC_ accession
YP_	Protein	Annotated on genomic molecules without an instantiated transcript record
XP_	Protein	Predicted model, associated with an XM_ accession
WP_	Protein	Non-redundant across multiple strains and species

Code status

Chaque enregistrement a un COMMENT, indiquant le niveau de conservation qu'il a reçu et l'attribution du groupe collaborateur. Ainsi, un enregistrement RefSeq peut être une copie essentiellement inchangée et validée de la soumission originale de l'INSDC, ou inclure des informations mises à jour ou supplémentaires fournies par des collaborateurs ou le personnel du NCBI. Voici tous les codes status RefSeq provenant de la Table 2 du
Chapitre 18 The Reference Sequence (RefSeq) Database retrouvé dans The NCBI Handbook

Code	Description
MODEL	The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to individual review or revision between annotation runs.
INFERRED	The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by experimental evidence. The record may be partially supported by homology data.
PREDICTED	The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.
PROVISIONAL	The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.
REVIEWED	The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.
VALIDATED	The RefSeq record has undergone an initial review to provide the preferred sequence standard. The record has not yet been subject to final review at which time additional functional information may be provided.
WGS	The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These records are not subject to individual review or revisions between genome updates.