Nuc-prot set

The Nuc-prot set, containing a nucleotide and one or more protein products, is the type of set most frequently produced by a Sequin data submission. The component Bioseqs are coimected by coding sequence region (CDS) features that describe how translation from nucleotide to protein sequence is to proceed. In a traditional nucleotide or protein sequence database, these records might have cross-references to each... 

Other to indicate this relationship. The Nuc-prot set makes this explicit by packaging them together. It also allows descriptive information that applies to all sequences (e.g., the organism or publication citation) to be entered once (see Seq-descr Describing the Sequence, below). 

A Seg set contains a segmented Bioseq and a Parts Bioseq-set, which in turn contains the raw Bioseqs that are referenced by the segmented Bioseq. This may constitute the nucleotide component of a Nuc-prot set. 

Descriptors were introduced in the NCBI data model to reduce redimdant information in records. For example, the protein products of a nucleotide sequence should always be from the same biological source (orgaiusm, tissue) as the nucleotide itself. And the publication that describes the sequencing of the DNA in many cases also discusses the translated proteins. By placement of these items as descriptors at the Nuc-prot set level, only one copy of each item is needed to properly describe all the sequences. 

A sequence record for a gene and its protein product will typically have a single BioSomce descriptor at the Nuc-prot set level. A population or phylogenetic study, however, will have BioSource descriptors for each component. (The components can be nucleotide Bioseqs or they can themselves be Nuc-prot sets.) The BioSources in a population study will have the same organism name and usually will be distinguished from each other by modifier information, such as strain or clone name. 

The remainder of the definition line, which is usually a title for the sequence, can be generated by software from features and other information in a Nuc-prot set. 

Figure 4.3. The NCBI Desktop displays a graphical overview of how the record is structured in memory, based on the NCBI data model (see Chapter 2). This view is most useful to a software developer or database sequence annotator. In this example, the submission contains a single Nuc-prot set, which in turn contains a nucleotide and two proteins. Each sequence has features associated with it. BioSource and publication descriptors on the Nuc-prot set apply the same organism Drosophila melanogaster) and the same publication, respectively, to all sequences.

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