Nucleotide databases

Entrez nucleotide database, June, 2006 (http //www.ncbi.nlm.nih.gov/entrez). 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

The secondary identifier is the "PROTEIN ID," which stands for the Protein Sequence Identifier. In nucleotide sequence entries, it is a string stored, in a qualifier called protein id, which is tagged to every CDS in the nucleotide database. Example ... 

The second approach is the tandem mass spectrometric method (Wilm et ah, 1996 Link et ah, 1999 Yates, 2000). This method relies on fragmentation of individual peptides in the tryptic peptide mixture to gain sequence information. Its main advantage is that sequence information derived from several peptides is much more specific for the identification of a protein than a list of peptide masses. The sequence data can be used to search not only protein sequence databases but also nucleotide databases such as expressed sequence tag (EST) databases and, more recently, even... 

EMBL Nucleotide Database (collection of nucleotide sequences). 

JR Yates III, JK Eng, AL McCormack. Mining genomes correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem 67 3202-3210, 1995. 

The most important sources of information for molecular modeling are the FDB fll5], the SwissPtot protein sequence database (138], the Gcnbank, and the EMBL nucleotide database. 

EMBL—the European Molecular Biology Laboratory (Heidelberg) Nucleotide Sequence Database (also known as EMBL-Bank). The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). The EMBL nucleotide sequence database is part of the Protein and Nucleotide Database Group (PANDA). 

Other useful addresses, especially in the context of research on allergens in the fields of proteomics and genomics, are the databases on sequences of nucleotides corresponding to particular proteins or epitopes, e.g., The EMBL Nucleotide Sequence Database—http //www.ebi.ac.uk/embl/Access/, or the Protein and Nucleotide Database Group (PANDA)—http //www.ebi.ac.uk/panda/ or the database Ensembl— http //www.ensembl.org/index.html, http //www.ebi.ac.uk/ensembl/. 

A general outline of the bottom-up mass spectrometry approach for proteome analysis is presented in Figure 3. In general, the mass spectrometry is performed at the peptide level after digesting the protein to obtain the molecular mass and amino acid sequence-specific ions, which are correlated with similar information in the protein or nucleotide database.7 16 Based upon these measurements, the following approaches have evolved. 

The EMBL database is a model nucleotide database to consider. Each entry in the database is given a unique ID and information about the entry is presented in a semi-structured way. The actual nucleotide sequence is presented at the end of the entry. 

Protein databases used to be from direct protein sequencing, but now they are made almost exclusively from the translation of ORFs (Open Reading Frames on DNA sequences). Both the European Bioinformatics Institute (EBI) and National Center for Biotechnology Information (NCBI) provide databases, TREMBL [15] and GENPEPT [19] respectively, which are automatic translations from the CDS features of the DNA in their nucleotide databases. This includes some automated annotation of the role which the protein plays. 

There are three varieties of translated BLAST search tblastn, blastx, and tblastx. In the first variant, tblastn, a protein sequence query is compared to the six-frame translations of the sequences in a nucleotide database. In the second variant, blastx, a nucleotide sequence query is translated in six reading frames, and the resulting six-protein sequences are compared, in turn, to those in a protein sequence database. In the third variant, tblastx, both the query and database subject nucleotide sequences are translated in six reading frames, after which 36 (6 x 6) protein blastp comparisons are made. Protein sequences... 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

The GBFF can be separated into three parts the header, which contains the information (descriptors) that apply to the whole record the features, which are the armotations on the record and the nucleotide sequence itself. All major nucleotide database flat files end with // on the last line of the record. 

---