In this section, you will use the NCBI Map Viewer and the keyword opsin to get a list of opsin or opsin-related genes in the human genome.
The subject of this tutorial is human opsins, which are found in the cells of your retina. Opsins catch light and begin the sequence of signals that result in vision. We will proceed by asking questions about opsins and opsin genes, and then using bioinformatics to answer them.
When I provide a web address, I'll also make it a link -- just click it to go to the site in a new browser window. Then make it a bookmark so you can find it again. This tutorial will still be open in the window behind the new one.
WARNING: Bioinformatics tools evolve rapidly, faster than I can make changes to this tutorial. So if a page does not look exactly like I say it should, or if its title is different, look around and try to do what the tutorial says. You should find the same links, but names may be slightly different, or many new links may have been added (bioinformatics pages never get simpler). If the differences are so great that you can't proceed, send me email (see contact link at top of Tutorial Contents), and I'll adapt the instructions to the changes as soon as I learn about them.
Point your browser to http://www.ncbi.nlm.nih.gov/mapview/. You find a list of organisms for which genome information is available. In the right-hand columns beside each organism are links to tools. Hold your mouse pointer on each tool symbol for a brief description of what it does.
Find Homo sapiens (human), and click on the magnifier tool beside the lowest-numbered Build (a build is an assembly of the genome, which is done repeatedly). We will use the older build because sometimes not all searching and viewing tools are not connected to the newest build, which is in progress. The magnifier tool takes you to the Search Page for the organism, which shows a chromosome diagram, and provides input boxes (at top of page) for searches.
In the box next to Search for, enter opsin.
You see the diagram again, with red marks at your "hits", the locations of genes whose entries contain "opsin" as a whole or partial word. Below the diagram is a list of the indicated genes.
If the list is very long, simplify it using Quick Filter box on the right at the top of the list; check the box marked Gene, and then click Filter. If you are already seeing the filtered list, the Quick Filter box will not be present.
In the list of genes related to the search term opsin, there are the rhodopsin gene (RHO), and three cone pigments, short-, medium-, and long-wavelength sensitive opsins (for blue, green, and red light detection). Four hits look like visual pigments, which should not surprise you. To the left of each entry is the chromosome number, allowing you to tell which red mark corresponds to each entry. Note that several hits are on the X chromosome, one of the sex-determining chromosomes.
NOTE: In the human genome lists, you will often see duplicates marked reference or Celera, referring to the results from two major efforts to sequence the human genome. At first, these two efforts were separate, but eventually they came together. When you have a choice, choose "reference," so you will be following the same path I followed in setting up the tutorial.
You can get more details on multiple hits on the same chromosome with the all matches link for that chromosome. Click all matches next to X. Be patient: the next page may load slowly--it's packed with information.
You see a very complicated display (don't sweat -- we're going to use only a part of this). On the left is a diagram of the X chromosome, with red marks at the positions of the gene(s) you've followed to this page -- in our case, the two opsins, medium- and long-wave, which are located near the bottom tip of the X chromosome. To the right are various representations of the X chromosome, with listings of annotated areas. The two opsin genes are highlighted in pink. If you pass your cursor over this page without clicking, you will find that some symbols provide brief information, mostly about regions that are not yet characterized well enough to have a full entry.
As you can see, there is a tremendous amount of information on this page, with links to much more. If you want full information about the meanings of abbreviations and symbols on this page, as well as the kinds of information linked to the page, you can use Map Viewer Help at the top of the page. You will find abundant information about the Map Viewer, explanations of all symbols and links, and even tutorials about how to ask and answer all kinds of questions about the genome. The Map Viewer is like the Google Earth of the genome, and as with Google Earth, the amount of information is sometimes daunting.
For now, note the information provided for the the opsin gene OPN1LW (called the gene symbol). You see that this is the long-wavelength-sensitive (red) opsin, and that it's a gene involved in color blindness (a sex-linked trait -- no surprise, because we find the gene on the X chromosome).