The RefSeq database provides a stable collection of genetic sequence information. It serves as a standard reference for nucleotide sequences, which include DNA and RNA, and their corresponding protein products. This publicly accessible database aims to offer a single, well-defined record for each biological molecule from various organisms, ranging from viruses and bacteria to eukaryotes. It provides reliable and consistent sequence data for the scientific community, supporting various research and clinical applications.
The Curation and Validation Process
The National Center for Biotechnology Information (NCBI) maintains the RefSeq database, ensuring high quality and reliability. This involves curation, where sequences are reviewed, standardized, and annotated by NCBI staff and automated computational pipelines. The goal is to establish a singular, non-redundant, and stable record for each distinct biological molecule, such as a gene, its transcript, and protein.
This process results in a non-redundant collection, meaning that for a given biological molecule, there is typically only one representative record, preventing confusion from multiple, potentially differing submissions. The records are designed for stability, providing a consistent reference that researchers can depend on over time for their experiments and analyses. NCBI’s ability to update these records as new information becomes available further enhances their utility as a current and precise description of biological sequences.
Distinguishing RefSeq from GenBank
RefSeq and GenBank are both biological sequence databases, but they serve different purposes. GenBank functions as an archival repository, collecting all publicly available sequence data submitted by scientists. GenBank can contain redundant entries, errors from original submissions, and represents a snapshot of the data as it was initially provided.
In contrast, RefSeq is a curated subset of sequence data, largely derived from GenBank and other international sequence databases (e.g., ENA, DDBJ). RefSeq records are created and refined by NCBI curators, integrating information from various sources to produce accurate and thoroughly annotated sequences. While GenBank is a vast public archive where anyone can deposit sequence data, RefSeq is a specialized reference section, offering the most refined and verified version of each unique biological sequence. This distinction underscores RefSeq’s role as a standardized and authoritative resource for researchers.
Structure and Accession Numbers
Every RefSeq record is assigned a unique identifier, an accession number, which provides a standardized way to reference specific sequences. Accession numbers typically begin with a two-letter prefix followed by an underscore and a series of digits. The prefix indicates the type of molecule or genomic region the record represents, offering insight into its content.
For instance:
NG_ denotes genomic regions, often representing a gene.
NM_ prefixes are used for messenger RNA (mRNA) sequences, which are transcribed from genes and carry instructions for protein synthesis.
NP_ accession numbers identify proteins derived from these mRNA sequences.
NR_ is reserved for non-coding RNA molecules, such as ribosomal RNA or transfer RNA.
XM_ and XP_ prefixes indicate computationally predicted sequences for mRNA and protein, respectively, which are models rather than experimentally verified sequences.
Each accession number also includes a version number, such as NM_000520.6, signifying that the record has been updated, maintaining accuracy and traceability.
Applications in Scientific Research
The RefSeq database serves as a foundational resource in scientific investigation. Its stable and curated sequences are used in genome annotation, where researchers employ RefSeq records as a reliable standard to identify and label genes, coding regions, and other features on newly sequenced genomes. This helps consistently map genomic elements across different studies.
In clinical genetics, RefSeq provides an unambiguous reference for reporting patient genetic variants. By referencing a specific RefSeq accession number and version (e.g., NM_000059.3), laboratories ensure genetic variations are described against a stable and universally recognized sequence, facilitating clear communication and comparability of results. Researchers use RefSeq as a starting point for various experiments, including designing primers for PCR amplification or investigating gene function. Using a common, verified reference sequence ensures that scientists are studying the same biological molecule, promoting consistency and reproducibility in scientific findings.