Nucleotides INDEX

EMBL European Bioinformatics Institute nucleotide sequence database biblio., sub- stance, se- quence 20mio nucleotide seq., 28billion nucleotides journals, author submis- sions European Bioinformatics Institute free daily http //www.e- hi.ac.uk/embl/ index.html... 

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/. 

BIBLIOGRAPHY OF CRYSTAL STRUCTURES OF CARBOHYDRATES, NUCLEOSIDES, AND NUCLEOTIDES FOR 1979 AND 1980 ADDENDA AND ERRATA FOR 1970-1978 AND INDEX FOR 1935-1980... 

An index of the phospho anhydride (i.e.,P—O—P) bond content of the adenine nucleotides of a cell, based on a hypothetical modeP that attempts to explain the metabolic basis for control of ATP utilization and regeneration. Later studies demonstrated that the energy charge model is overly simplistic and that its principles are unlikely to constitute a useful model for the control of energy metabolism within biological systems. 

Cyclophosphamide (Cytoxan) is the most versatile and useful of the nitrogen mustards. Preclinical testing showed it to have a favorable therapeutic index and to possess the broadest spectrum of antitumor activity of all alkylating agents. As with the other nitrogen mustards, cyclophosphamide administration results in the formation of cross-links within DNA due to a reaction of the two chloroethyl moieties of cyclophosphamide with adjacent nucleotide bases. Cyclophosphamide must be activated metabofically by microsomal enzymes of the cytochrome P450 system before ionization of the chloride atoms and formation of the cyclic ethylenimmonium ion can occur. The metabolites phosphoramide mustard and acrolein are thought to be the ultimate active cytotoxic moiety derived from cyclophosphamide. 

Fermentation industry. Primary metabolites of importance in ihe fermentation field include amino acids, purine nucleotides, vitamins, and organic acids. Specific products include citric acid, riboflavin (vilamin B>). and cubalamin (vilamin B12). Check alphabetical index pertaining lo specific vitamins. Of the secondary metabolites, antibiotics are Ihe mosl... 

The NCBI s Entrez is apowerful database search engine. This integrated search engine provides a menu (http //www.ncbi.nih.gov/Entrez/index.html) offering the user selections to search biomedical literature (PubMed), databases on OMIM, nucleotide sequence, protein sequence, whole genome sequences, 3D macromolecular structures, taxonomy (organisms in GenBank), SNP,... 

The ID nucleotide/amino acid sequences in character format (without index, e.g., fasta format) can be converted into the 2D chemical structures with ISIS Draw, which can be downloaded from MDL Information System at http //www.mdli.com/ download/isisdraw.html for academic use. Install the package by issuing Run command, C Isis Draw23.exe. Launch IsisDraw to open the Draw window. 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

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/. 

Henceforth, crystal structure analyses of carbohydrates (class 45), amino acids (class 48), purines and pyrimidines (class 44) and nucleosides and nucleotides (class 47) are referenced by means of their Cambridge Crystallographic Data Base REFCODES. All other crystal structure analyses are referenced in the General Index. 

Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation. URL http //www.ncbi.nlm. nih.gov/SNP/index.html. Uses SNP in the much looser sense of minor genetic variations and includes microsatellite repeats and small insertion/deletion polymorphisms. 

GeneSeq . Thomson Derwent s biosequence database, provides information on nucleic and amino acid sequences found in the patent literature. It has biosequence indexing for the patents included in the DWPI database beginning with the very first patents to carry protein and nucleotide sequence descriptions. GeneSeq structure searches retrieve records with the sequence, a short abstract directed to that sequence. 

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