GenBank genomes

This is fundamental to the progress of genomics (and many other areas) of science. Generating data in a common exchangeable format, with a common lexicon of terms [47] in a single non-redundant location is a major goal. A number of examples exist, such as the DNA and protein sequence data in GenBank, EMBL or SwissProt [48-50]. 

HPME SEHPCH HITFMAt PubMed 1 All Databases 1 Human Genome i GenBanK 1 Mao Viewer 1 BLAST ... 

If PMF and sequence homology searches fail using available protein and EST databases, mass spectrum data can, in principle, be used to search genome databases (GenBank http //www.ncbi.nlm.nih.gov/). However, only a small percentage of large genomic sequences code for proteins such that bioinformatics still needs to accurately define exon-intron structures (Andersen and Mann, 2000). 

One point to remember when exploring either genomes or GenBank nucleotide entries, searchers should be aware that, especially in GenBank, there exist multiple entries for the same gene and this confuses links between the gene of interest,... 

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,... 

These pages provide links to larger resource categories such as GenBank, Molecular databases, Genomes and Maps, Tools, Software engineering, and FTP sites. There is also a table with a comprehensive alphabetical index of Web resources. 

In addition to automated functional annotation of putative 5-HT receptor sequences, determination of open reading frames (ORFs), start codons, and intron/exon boundaries from genomic sequences is now also automated. The absence of expert human curation in such automated annotation can potentially lead to the presence of incorrect sequence data in the databases that has arisen from misidentification of ORFs, start codons, and intron/exon boundaries in raw genomic sequences. For example, the sequences of several chimpanzee 5-HT receptors have recently been added to the GenBank databases, but the sequences given for these receptors indicate that one or several of the seven transmembrane (TM) helices are not present in the sequence, although... 

Figure 1 Predicted sequence and membrane topography of the murine delta opioid receptor. The mouse sequence was obtained from Genbank (accession No. L07271). Negatively charged amino acids within TMD 2 and 3 are circled and extracellular N-linked glycosylation sites are indicated ( ). Arrows indicate intron/exon boundaries in the mouse genome. (From Ref. 40.)...

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