GenBank sequence database

GenBank (NCBI, USA) EMBL Nucleotide Sequence Database (Europe) DDBJ (Japan) The three main nucleotide sequence databases, which are synchronised daiiy... 

Salutaridinol 7-O-acetyltransferase was purified to apparent electrophoretic homogeneity from P. somniferum cell suspension cultures and the amino acid sequence of ten endoproteinase Lys-C-generated peptides was determined.28 A comparison of these amino acid sequences with those available in the GenBank/EMBL sequence databases indicated no relevant similarity to known proteins. The first attempt to isolate a cDNA encoding salutaridinol 1-0-... 

PIR provides also some degree of crossreferencing to other biomolecu-lar databases by linking to the DDBJ/EMBL/GenBank nucleotide sequence databases, PDB, GDB, FlyBase, OMIM, SGD, and MGD. 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

We design primers by aligning homologous sequences Ifom as many taxa as possible. These sequences can be readily retrieved from large sequence databases such as Genbank (http //www.ncbi.nlm.nih.gov/web/... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

The sequence of the gene can be used to deduce the amino acid sequence of the protein encoded by the gene. The DNA and amino acid sequences can then be used to identify similar sequences in the large sequence databases such as GenBank (www.ncbi.nlm.nh.gov) or SWISSPROT (www.expasy.org). The chemical data obtained form the mutant combined with the sequence data from the gene that is defective in the mutant can then provide information on the function of the gene in the biosynthesis of a certain class of phenolic compounds. 

GenBank is the NIH genetic sequence database, and an annotated collection of all publicly available DNA sequences. It is part of the International Nucleotide Sequence Database Collaboration, which comprises the GenBank at NCBI, DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL). These three organizations exchange data on a daily basis. 

One of the central activities of the European Bioinformatics Institute (EBI) (Emmert et ah, 1994) is development and distribution of the EMBL nucleotide sequence database (Stoesser et ah, 2001). This is a collaborative project with GenBank (NCBI, USA) and DDBJ (DNA database of Japan) to ensure that all the new and updated database entries are shared between the groups on a daily basis. The search of sequence databases and an access to various application tools can be approached from the home page of EBI at http //www.ebi.ac.uk/ (Figure 3.3). 

The nucleotide sequences can be retrieved from one of the three IC (International Collaboration) nucleotide sequence repositories/databases GenBank, EMBL Nucleotide Sequence Database, and DNA Data Bank of Japan (DDBJ). The retrieval can be conducted via accession numbers or keywords. Keynet (http // www.ba.cnr.it/keynet.html) is a tree browsing database of keywords extracted from... 

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). 

---