DDBJ records

Recently, the members of the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ) introduced a better sequence identifier, one that combines an accession (which identifies a particular sequence record) with a version number (which tracks changes to the sequence itself). It is expected that this kind of Seq-id will become the preferred method of citing sequences. 

Although the DDBJ/EMBL/GenBank feature table allows numerous kinds of features to be included (see Chapter 3), the NCBI data model treats some features as more equal than others. Specifically, certain features directly model the central dogma of molecular biology and are most likely to be used in making coimections between records and in discovering new information by computation. These features are discussed next. 

A full release of GenBank occins on a bimonthly schedule with incremental (and nonincremental) daily updates available by anonymous FTP. The International Nucleotide Sequence Database Collaboration also exchanges new and updated records daily. Therefore, all sequences present in GenBank are also present in DDBJ and EMBL, as described in the introduction to this chapter. The three databases rely on a common data format for information described in the feature table documentation (see below). This represents the lingua franca for nucleotide sequence database annotations. Together, the nucleotide sequence databases have developed defined submission procedures (see Chapter 4), a series of guidelines for the content and format of all records. 

DNA sequence records from the public databases (DDBJ/EMBL/GenBank) are essential components of computational analysis in molecular biology. The sequence records are also reagents for improved curated resources like LocusLink (see Chapter... 

Many biological databases (databanks) are embedded with tutorials that make it easy to explore their facilities. There are three sources of biological databases in-house dedicated sources (private and limited for focused projects), databases assembled by companies (mainly fees for services extensive and high-quality but expensive and restrictive such as Celera Genomics and Incyte Genomics), and public databases (such as GenBank, EMBL and DDBJ). An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation (Table 14.11). Their record is the sequence or structure as it was experimentally derived. 

The 3D-1D compatibility algorithm (Ito et ai, 1997) is applied to predict the secondary structures by threading at SSThread of DDBJ (http //www.ddbj.nig.ac.jp/E-mail/ ssthread/www service.html). The threading result reports the anuno acid sequence with the predicted secondary structures (H for a-helix E for -strand and C for coil or other). The threading prediction of the query sequence against the structural library chosen from PDB at LIBRA I (http //www.ddbj.nig.ac.jp/E-mail/libra/LIBRA I.html) reports a list of compatible structures and 3D-ID alignment results recording the secondary structures and accessibility. 

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