The Bioinformatics Blog

Firefox?!?!

I know what you’re thinking. “Come on. A browser? As a bioinformatics tool?” You might actually be surprised. I think that most people that do research spend at least some amount of time online trying to track down information. Maybe it’s  protein name, or DNA elements in a chromosome segment. Maybe it’s a certain paper or topic through PubMed. Personally, I spend a good amount of time searching out answers. Furthermore, I switch between databases / websites between tabs to get information from different sources. Could there be a way to search faster?

Keyword Search To The Rescue!

Luckily, there is a faster way: the keyword search. Basically the keyword search will allow you to make a bookmark shortcut to any search box using a keyword. Once a keyword search has been saved that particular search can be invoked with just the keyword. I frequently use the UCSC Genome Browser for research, so I’ll use this as an example.

How To

1. Navigate to the UCSC Genome Browser main page.
2. In the top navigation panel click “Genomes”
3. The default page should be the Human genome browser. If you are interested in a different organism you can certainly change it using the drop-down boxes. There should be an input box labeled “position or search term”. Right click in the box.
4. In the pop-up menu select “Add a Keyword for This Search…”. An “Add Bookmark” window will appear.
5. In the “Name” box type a descriptive name. In this case use “UCSC Human Search”.
6. In the “Keyword” box type the keyword you want to use. In this case use “ucsc”.
7. Press the “Add” button to save this search.

Let’s test the keyword. Open a new blank Firefox tab by pressing CTRL+T or File -> New Tab. In the address bar type “ucsc MECP2″ and press enter. The “ucsc” keyword triggers the query “MECP2″ to be run through the search box we saved. After a few seconds a window for the UCSC browser should appear listing possible genes matching the symbol MECP2. If you had navigated to the UCSC Browser directly and typed MECP2 directly in the search box the results would have been the same.

What about direct chromosome positions? Let’s try it. Clear the text from the URL bar, type “ucsc  chr1:1-20000000″, and press enter. The page should change to show the first 20,000,000 base pairs of chromosome 1.

What other uses could it have? What about a “pubmed” keyword search? Or an Ensembl search? It can be particularly powerful of you combine these searches. If you were researching Rett Syndrome, you could in one tab search for “pubmed Rett Syndrome”. After reading a few papers and finding information on MECP2 in Rett Syndrome all you have do is hit CTRL+T to open another tab. Then type “ucsc MECP2″ to find it in the genome browser. If you had a saved search for the NCBI Protein database you could go even further by opening yet another tab and typing “protein MECP2_HUMAN” (assuming your keyword was protein). The result would be a page about the MECP2 protein in humans where you could get the amino acid sequence. Your specific search set would depend on what databases you search most frequently in your research.

This kind of time savings can really add up. Plus you can show off your cool new hack to friends when they’re trying to search for something.

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