Primary accession number

FIGURE 1.1 A 2D-gel electrophoresis map of colorectal epithelia cells proteins from the SWISS- 2DPage database (entry CATD HUMAN, primary access number P07339) accessible from http //www.expasy.org/swiss-2dpage. 

There are no duplicate primary accession numbers between SWISS-PROT and TrEMBL, because they are sharing the same system of accession numbers. A TrEMBL entry (and its associated accession number (s)) can either move to SWISS-PROT as a new entry or be merged with an existing SWISS-PROT or TrEMBL entry. In the latter case, the accession number (s) of that TrEMBL entry are added to that of the SWISS-PROT entry. 

Figure 1 Domain map of the steroid receptor. The numbers correspond to residues of the human glucocorticoid a receptor at the boundaries of the regions identified in the schematic diagram. Source PubMed Primary accession number P04150.

Chromosomal Location (OMIM) Number of Amino Acids (including signal peptide) Gene Name Swiss-Prot Entry Name (primary accession number) Notes... 

The mass differences in the b series reveal the presence of L/I followed by S in the sequence. This information is sufficient to attempt a sequence tag search. Searching the SwissProt database for H. sapiens proteins by entering m/z 1833.9 for the parent ion and 1108.5, 1021.5, and 908.4 for the b series fragments in the MS-Seq searching tool of Protein Prospector [11] turns up a single protein, human hemoglobin a subunit with primary accession number P69905. 

The database identifier is the name of the database that contains the linked entry. The primary identifier (in most cases the accession number) is the entry s primary key, while the secondary identifier complements the information given by the first identifier. The currently linked databases are listed in Table II. 

The work of C.G. Dunkle found in his Syllabus (1957/1958) issued in typewritten form by Picatinny Arsenal Library, Dover, NJ (Accession Number U48378) and Syllabus (1960-196 1), contg additions and corrections to the earlier syllabus, were very helpful, especially for locating primary sources of information. Syllabus (1960-1961) can be obtd as AD 290417 from the Defense Documentation Center, Defense Supply Agency, Cameron Station, Alexandria, Virginia, 22314. US Bureau of Mines... 

Databases are electronic filing cabinets that serve as a convenient and efficient means of storing vast amounts of information. An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation. Their record is the sequence as it was experimentally derived. The DNA, RNA, or protein sequences are the items to be computed on and worked with as the valuable components of the primary databases. The secondary databases contain the fruits of analyses of the sequences in the primary sources such as patterns, motifs, functional sites, and so on. Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier (i.e., an entry name and/or accession number) so that it can be retrieved uniformly by the combination of the database name and the identifier. 

Table 1 contains a summary of all these structures, including accession numbers in the PDB [35] and NDB [36], and the primary references. 

The accession number, on the third line of the record, represents the primary key to reference a given record in the database. This is the number that is cited in publications and is always associated with this record that is, if the sequence is updated (e.g., by changing a single nucleotide), the accession number will not change. At this time, accession numbers exist in one of two formats the 1 + 5 ... 

PDB from J. Sussman, D. Lin, J. Jiang, N, Manning, J. Ptilusky, O. Ritter, and E. Abola, Acta Crystallogr. D54,1078 (1998) Research Collaboratory for Structural Bioinformatics PDB, http //www.rcsb.otg/pdb/] as of October 1999. The year of submission of the cowdinates (year), the PDB accession number (PDB ID), resolution, and R-factor of the crystal structure refinement (Res and R-factor, respectively) the name and host organism of the protein and the primary structure reference (if published) and the source of the protein [i.e., either wild-type (wt) or recombinant (rec)], are indicated for each structure. Coordinate sets on hold are listed at the end of the year they were submitted. Structures were found via keyword searches that should identify most, but perhaps not all, of the relevant sets of hypertheimophilic proteins in the PDB. 

The unique accession number given to a sample on receipt follows it through the analytical phase to the production of the final report. Machines with bar-code reading capability can read bar-coded laboratory accession numbers and link these with associated reports for these patients via computer interfacing. This allows the production of a cumulative report from which disease trends can be assessed. Bar-coded primary sample tubes (i.e., no aliquoting) can be handled on these analyzers. 

Owing to the high workloads (often 2000 or more samples per day), samples are uniquely identified with a laboratory accession number. If serum or plasma is required, the blood sample is centrifuged (at 3000rpm) and the serum or plasma may be removed but primary tube sampling is now prevalent and a gel separator allows pouring off of the supernatant if desired (see the section Large-capacity analyzers ). 

A number of structured databases have been developed to classify proteins according to the three-dimensional structures. Many of these are accessible via the World Wide Web, T1 protein databanlc (PDB [Bernstein d al. 1977]) is the primary source of data about the stru tures of biological macromolecules and contains a large number of structures, but many i these are of identical proteins (complexed with different ligands or determined at differet resolutions) or are of close homologues. 

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