Читать книгу Bioinformatics - Группа авторов - Страница 22

The first several chapters of this book describe a variety of ways in which sequence data and sequence annotations find their way into public databases. While the combination of data derived from systematic sequencing projects and individual investigators' laboratories yields a rich and highly valuable set of sequence data, some problems are apparent. The most important issue is that a single biological entity may be represented by many different entries in various databases. It also may not be clear whether a given sequence has been experimentally determined or is simply the result of a computational prediction.

To address these issues, NCBI developed the RefSeq project, the major goal of which is to provide a reference sequence for each molecule in the central dogma (DNA, mRNA, and protein). As each biological entity is represented only once, RefSeq is, by definition, non-redundant. Nucleotide and protein sequences in RefSeq are explicitly linked to one another. Most importantly, RefSeq entries undergo ongoing curation, assuring that the RefSeq entry represents the most up-to-date state of knowledge regarding a particular DNA, mRNA, or protein sequence.

RefSeq entries are distinguished from other entries in GenBank through the use of a distinct accession number series. RefSeq accession numbers follow a “2 + 6” format: a two-letter code indicating the type of reference sequence, followed by an underscore and a six-digit number. Experimentally determined sequence data are denoted as follows:

NT_123456	Genomic contigs (DNA)
NM_123456	mRNAs
NP_123456	Proteins

Reference sequences derived through genome annotation efforts are denoted as follows:

XM_123456	Model mRNAs
XM_123456	Model proteins

It is important to understand the distinction between the “N” numbers and “X” numbers – the former represent actual, experimentally determined sequences, while the latter represent computational predictions derived from the raw DNA sequence.

Additional types of RefSeq entries, along with more information on the RefSeq project, can be found on the NCBI RefSeq web site.