- compare the type of information you retrieve in Entrez nucleotides and Entrez Genomes when searching for records from a particular organism, using human as an example:
- search Entrez Nucleotides for "human" in the Organism field
- how many nucleotide records are retrieved?
- search Entrez Genomes for "human" in the Organism field (or click on Homo sapiens on the "Prominent Organisms" page of Entrez Genomes)
- how many Genome records are retrieved?
- why is there such a large difference in the number of human records retrieved from the two Entrez databases?
- view the summary for human chromosome 7 and find detailed information for the cystic fibrosis transmembrane conductance regulator gene
- from the list of Entrez Genomes records retrieved for human, click on the accession number of chromosome 7 to display the summary information for that chromosome
- enter "cystic fibrosis" (without the quotes) in the search box near the top of the page to retrieve records from LocusLink that contain those terms
- what two genes are retrieved?
- click on the LocusID number of each item retrieved to see more detail about it
- which gene is for the cystic fibrosis transmembrane conductance regulator protein? That is, what is the official gene symbol, and what are the alternate gene symbols?
- what is the number of the OMIM record that summarizes the literature about that gene?
- what is the cytogenetic map location of the gene?
- what is accession number of the RefSeq mRNA record?
- what is accession number of the RefSeq protein record?
Advanced:
- remember that a cytogenetic map is only one type of map. LocusLink also provides links to map locations on other types of maps, when available, that use different scales.
- Follow the links for a few of the STS markers. Notice that a number of the markers are from the National Human Genome Research Institute's map for chromosome 7 ("NHGRI-7 Map"). Two of the other markers, sts-M28668 and SHGC-9783 are from GeneMap'99, the radiation hybrid map also known as "Gene Map of the Human Genome."
- what is the centiRay position of each GeneMap'99 marker, sts-M28668 and SHGC-9783?
- what is the reference interval into which each GeneMap'99 marker falls?
- if the markers come from the same gene, and therefore are from the same part of the chromosome, why is there such a big difference in the centiRay value?
- which of the markers was mapped with a higher confidence level?
- retrieve the Escherichia coli genome from Entrez Genomes by using the prominent organisms list or searching the "Organism" field
- Entrez will display an overview of the complete genome, with a graphic showing the distribution of genes on the inner and outer strands of the DNA, and the gene symbols of a few landmark genes
- find the location of the dnaK (heat shock) gene by entering "dnaK" (without the quotes) in the search box labeled "Search for gene"
- Entrez zooms you in to the part of the genome that contains dnaK, shows you the location in bases, and shows some surrounding genes
- what is the approximate location of the dnak gene in Kilobases (Kb)?
- what genes are immediately upstream and downstream of dnaK?
- scroll down the page to see a small graphic showing an overview of the E. coli genome. A red line shows the "slice" of the genome at which are we looking. Where in the genome are we looking, e.g., twelve o'clock, three o'clock eight o'clock?
- using that small overview graphic, click on the region at about 6 o'clock to see a detailed view of that region
- what is the location of that region in bases?
- what are some of the genes in that region?
- going back to the Entrez Genomes home page, retrieve the record for
the Human immunodeficiency virus type 1
- what is the total size of the genome?
- what other resources does NCBI have for HIV researchers? (hint: use NCBI Site Map)
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