HSLS Update

NCBI Genome Biology Resources

Genome Biology, the study of the genome -- the complete DNA sequence of all the chromosomes present in an organism -- offers enormous insight for understanding the complex biological processes at the molecular level. The availability of an organism's entire genome sequence allows scientists to identify and manipulate genes involved in major biological processes like metabolism, cellular differentiation, development and disease.

The first genomic sequence, the RNA bacteriophage MS2, was accomplished in 1976. In 1995, the first genomic sequence of an autonomous living organism was completed for the bacterium Haemophilus influenzae. A landmark was reached in 2003 when the complete human genome was sequenced. To date, 260 genomes have been completely sequenced and published including 21 archaeal, 206 bacterial, and 33 eukaryotic genomes.

The low cost and improved technology in DNA sequencing processes have been instrumental in the success of whole genome sequencing projects, which generate sequence information at an exponential rate. The National Center for Biotechnology Information (NCBI) has developed several noteworthy resources to decipher genome biology information. These include Entrez Genome Project Database, Map Viewer and Entrez Genome.

Entrez Genome Project Database
www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj is a collection of complete and incomplete large-scale sequencing projects for cellular organisms. This searchable database provides views of a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps.

The NCBI Map Viewer
www.ncbi.nlm.nih.gov/mapview/ offers genomic sequence browsing capabilities for a selected group of organisms. Using Map Viewer, you can view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.

Entrez Genome
www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome provides access to genomic data contributed by the scientific community for species whose sequencing and mapping is complete or in progress. It offers a unified graphical view of genetic and physical maps as well as sequence data for a selected organism.

The illustrated guide below provides an example for locating complete microbial genomic sequence information with all annotations. HSLS will offer a hands-on workshop, Introduction to Genome Browsers on June 8, 2005, which will provide further techniques for browsing genome sequence information. Check the HSLS class calendar www.hsls.pitt.edu/services/instruction/calendar for additional class offerings, or you may schedule a group or individual consultation with Ansuman Chattopadhyay, PhD, HSLS information specialist in molecular biology and genetics (ansuman@pitt.edu or 412-648-1297). Visit the HSLS molecular biology and genetics Web portal at www.hsls.pitt.edu/guides/genetics/ for more molecular biology and genetics resources tools, resources and tutorials.

Example: Searching Entrez Genome to locate a complete genomic sequence

The year 1995 marked the birth of a new era in biology, when the complete DNA sequence of an autonomous living organism, Haemophilus influenzae, became available. To find the complete genomic sequence for Haemophilus influenzae, follow these steps:

Go to Entrez Genome
www.ncbi.nlm.nih.gov/entrez/
query.fcgidb=Genome

Type Haemophilus influenzae [organism] and click GO.

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Six results appear with genomic sequences for different strains of Haemophilus influenzae, containing both complete and incomplete sequences. Select the top most result, NC_000907, which represents the complete genome sequence of Haemophilus influenzae, Rd KW20.

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The top portion of the result page provides hyperlinks to retrieve DNA sequence, annotation such as protein coding genes, structural RNA and software tools for comparative genomic analysis.

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The bottom portion of the results page provides a graphical overview of all protein coding genes organized in functional categories, such as DNA replication, lipid metabolism, etc. To see map locations of genes, click on a region of the map to zoom in on that region.

--Ansuman Chattopadhyay