Gene Data Bank

Sequences of the genes/cDNAs can be retrieved from databases on the Internet at various web sites. For example, GeneBank (at the National Center for Biotechnology Information, NCBI) is at http //www.ncbi.nlm.nih.gov/ Web/Search/index.html. The EMBL Nucleotide Sequence database (through the European Bioinformatic Institute, EBI) can be found at http //www.ebi.ac.uk/queries/queries.html, whilst that of the DNA Data Bank of Japan is at http //www.ddbj.nig.ac.jp/. 

The sequence data is compared to one or more of a proprietary (Microseq) or public (GenBank, http //www.ncbi.nlm.nih.gov EMBL Nucleotide Sequence Databank, http //www.ebi.ac.uk/embl/ DNA Data Bank of Japan (DDBJ), http //www.ddbj.nig.ac.jp/) database for identification. Frequently, only a portion of the gene, such as the internal transcribed spacer (ITS) regions, especially the ITSl region of SSU rDNAl 30>55.56,58,59 variable D2 region of the LSU rDNA,l >53... 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

Fig. 5. Circular plot of features of the Escherichia coli K12 genome generated by Jena Prokaryotic Genome Viewer. The maxima and minima of the purine excess are located in the sequences ranges (maximum 1.548.120-1.550.620, minimum 3.929.072-3.931.572). The orbit descriptions are mostly self-explanatory. CDS [PDB] stands for genes for which three-dimensional protein structures are available in the Protein Data Bank. Note, that the origin of replication correlates with the purine excess minimum. In the original coloring scheme the CDS(+) and CDS(—) orbits are colored according to COG functional categories. All other orbits have a uniform color.

Determination of Amino acid Sequence from DNA sequence. Understanding genetic codes and our ability to sequence nucleotides in a DNA segment made it possible to decipher the amino acid sequence of a protein encoded by a gene. It became customary to infer the amino acid sequences of different proteins as soon as the DNA sequence data became available in the gene bank. The primary structure of a large number of proteins deposited in the protein data bank (PDB) is obtained directly from the DNA sequence data. 

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