Entrez system

Welcome to O fflLl, Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBL the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources atNCBI and elsewhere. 

The primary interface to PubChem data is through the NCBI search engine, Entrez. This web-based interface is simple, yet powerful, with many features not immediately apparent to those unfamiliar with the Entrez system. This section is intended as both an introduction and a guide to the more advanced Entrez features, and the types of Entrez PubChem queries that can be performed. 

The best way to illustrate the integrated natiue of the Entrez system and to drive home the power of neighboring is by considering two biological examples, using the Web version of Entrez as the interface. 

Figure 7.11. The structure summary for IHMF, resulting from a direct query of the structures accessible through the Entrez system. The entry shows header information from the corresponding MMDB entry, links to PubMed and to the taxonomy of the source organism, and links to sequence and structure neighbors.

Entrez system http //www3.ncbi.nlm.nih.gov/Entrez/... 

Entrez (http //www.ncbi.nih.gov/entrez), information retrieval system, integrating NCBI databases of protein and nucleotide sequences, genomes, macromolecular stmctures, and MEDLINE literature database. 

All the data are from the Genome Division of the Entrez retrieval system (http // www.ncbi.nlm.nih.gov/Entrez/Genome/org.html). 

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

Searching through Databases Applications of network BLAST server, 266, 131 Entrez molecular biology database and retrieval system, 266, 141 applying motif and profile searches,... 

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... 

Retrieve one sequence (either DNA or protein) each from three major database retrieval systems—Entrez, SRS of EBI, and DBGet—and compare their outputs. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

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. 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

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