A genome browser is a web interface used to view the physical map of a chromosome. This map shows how much DNA separates two genes, as measured in base pairs. Human chromosomes range in size from 50 million to over 250 million base pairs. A genome browser shows schematic representations of entire chromosomes as well as "zoomed in" schematics of single genes and even the actual base pair sequence.
A genome browser allows the user to scroll across a chromosome and zoom in on certain locations. Many genome browsers allow the user to zoom in at the level of viewing the actual DNA sequence, although the real utility of a browser is in the ability to view genes in their larger context, rather than view the DNA sequence at the nucleotide level. The average size of a gene is 3,000 base pairs, so when zoomed in at the base pair level, the user will see less than an entire gene. The largest human gene, dystrophin, is 2.4 million base pairs long.
In addition to viewing schematic representations of genes, genome browsers may also show other useful information. This can include the portion of the gene that is translated into protein, called the mRNA, and DNA sequences that have functions other than coding for protein. The genome browser may also show which segments of DNA were used in the process of sequencing the genome.
A large number of organisms have sequenced genomes. There is no single browser that is standard to the field of genomics, so genome browsers may vary between sequenced genomes. Genome browsers have the function of being able to search for genes or sequences of interest, allowing the user to jump from one genomic location to another. It would not be efficient to scroll across a chromosome to get to a location of interest, because of the very large size of most chromosomes.
Some genome browsers have tools called gene sorters. This tool displays a table of genes that are related to each other. The relationship can be one of several types: sequence homology, similar expression profile, or genomic proximity. The user searches for a gene using a word or phrase, selects the type of relationship he or she would like, and the gene sorter displays the results of the search.
