Get Your Web Browser Up to Genomics Speed

    This book has many references and questions that require you to use the world wide web (WWW). The WWW was designed to use uniform standards so everyone would have equal access to all information. Unfortunately, a number of companies developed proprietary versions that do not work on all computers. In addition, new technology has been added to the original list of ways to deliver information. Therefore, this web appendix provides you with the information you need to get your computer up to speed for all the WWW sites used in Discovering Genomics, Proteomics and Bioinformatics.

Terminology
There are some basic terms that you need to know to use the links in this book. A more complete list can be found at this location <http://www-personal.umich.edu/~zoe/Glossary.html>.

Browser - a software program that allows you to visually surf the WWW. There are two main browsers: Netscape and Internet Explorer.

URL - Uniform Resource Locator which is a technical way of saying the web address. It is the string of letters, slashes and numbers that allow your browser to see the appropriate page. With newer browsers, you no longer have to type in the "www" portion of the address, though it never hurts to add it.

Frames - When a web page is divided into sections, each section is called a frame. If you visit <http://bio.davidson.edu/courses/Molbio/websearch/SearchingNCBI.html>, you will see two frames of equal size, though the left frame has a lot of text and the right frame says "Web pages from NCBI will appear here....."

Download - to retrieve software or other computer files from a remote location to your computer. For example, you will need to download some software to see certain web page.

Java - this is a programming language that sends a small program over the WWW to run locally on your computer. Java programs are called "applets" meaning small applications or programs. Java is the major area where standards are not respected. Macintosh computers that run operating system 10 (called OS X) are reported to support all forms of Java, both the original standard and the Microsoft derivations. Mac OS 9.1 and earlier only supports the original Java standards. PCs running Microsoft windows operating systems will be able to support both the original and the Microsoft derived forms of Java.

Plug-ins - these are free software add-ons that you can download to update your browser. Plug-ins are needed for some of the newer media for delivering sound and movies.

Browsers and Platforms
     There are two  major computer platforms in the biology world - Macintosh and PC (which stands for personal computer, also known as IBM-compatible or Microsoft products). A new comer to the field is Linux, and its popularity is growing among those who like to tinker and hack with computers. Since most Linux users also run another platform and because many plug-ins are not available for Linux, only Macintosh and PC platforms will be addressed here.

Macintosh Users
     Macintosh is still popular with many biologists but due to the power of Microsoft, it has some problems interpreting pages created with Microsoft standards. Furthermore, Mac users are a small minority of world users and so browser developers do not always test their products on Macintosh computers. Because of these two reasons, Mac users will probably want to download both Netscape and Internet Explorer (often abbreviated IE).

     One final note about Macintoshes. As with all computers, the number of programs you can run simultaneously is determined by the amount of RAM you have bought. With Macs, you can set the RAM for each program individually so that you can have more than one open at a time even with very little RAM. However, the down side to this approach is that some big files may not open and you may get an error message. If this happens, you can fix the problem by finding the application that is RAM-limited and click on it once to highlight it but not launch it (you must quit the application if it is already running). Once the application is highlighted, hold down the Apple key and type the letter I while still holding down the apple key. This will bring up a window as shown in figure 1-1.

     Click in the box next to show: and choose memory. From this window, you can increase the allocation of RAM for any application. In this example (figure 1), the RAM is set for 40,312 K (or 40.312 megabytes). This is much higher than the default setting of 8192 and allows larger files to be viewed.

Netscape
    To download the latest version of Netscape, go to the Netscape download home page <http://home.netscape.com/products/index.html?cp=brinavbrincs>. As of this writing, Netscape version 6.1 is still in early form (called beta). Since there might be some bugs (problems) with this version, this book will assume you are using 4.x which means the most recent version of Netscape 4. The current version is called 4.78. Download this by clicking on the link that says "Netscape Browsers" and follow the directions. By the time the book is published, version 6.x may be the only  option available. If so, download Netscape 6.x.

     Another advantage for Netscape is the built in composer function. Netscape Composer is a free web authoring program which allows you to create your own web pages. Unless you have access to another product, you can use Composer free of charge for your web pages.

IE
     The only advantage IE has over Netscape on a Mac is Java applications. Due to Microsoft's position in the market, it can set its own standards and expect a majority of the world to conform. This means that only the Microsoft browser IE 5.x and later will work with Microsoft Java applets. The newer versions of Microsoft Java (1.1 and 1.2) may only work on Macintoshes that run with OS X. This means in a few more years, this Java v. MS-Java conflict will fade into the distant past.

    Due to an agreement between Apple and Microsoft, IE is preloaded on newer machines. If you cannot find it, download IE by going to the Microsoft web page for browsers <http://www.microsoft.com/windows/ie/default.htm>. Click on the download button and follow directions. The current version is 5.5 and soon version 6.x will become the new standard. Download which ever is available.

PC Users
     For PC users, Windows comes with IE built in. IE performs most functions properly. The only exception may be chime which will be discussed below. If you need to update your version of IE, you can go to the download page at this URL <http://www.microsoft.com/windows/ie/default.htm>. Click on the appropriate button and follow the directions. Netscape does work on PC's as well and you can obtain a copy from the Netscape Home Page <http://home.netscape.com/computing/download/index.html?cp=hop05hb2>.

Searching a Web Page for a Particular Term
     Here is a simple problem with a simple solution. Have you ever searched a web page for a particular word and had trouble finding the word after viewing the right web site? To find the word, you can simply use the "Find" function of your web browser and it will find the word for you. This is especially helpful on web pages that have a lot of text.

Sample using Find function
     Go to this URL  at Cold Spring Harbor <http://www.nobel.se/chemistry/laureates/index.html>. Up at the very top of your window, click on the "Edit" menu and choose "Find". When a dialog box appears, type in the word "Mullis" and hit return. You will see the word highlighted on the page. This is an easy way to find the content you are looking for rather than having to scroll down long pages.

Optimizing Your Browser

There are a few web sites that stand out as places to start. We will visit a few of them here with other sites listed at the end of this chapter.

Entrez PubMed - http://www.ncbi.nlm.nih.gov/PubMed/
     The first place to start any project is the previously published literature. Go to the Entrez PubMed web site to search the biomedical literature. This is run by the National Center for Biotechnology Information <www.ncbi.nlm.nih.gov> which is a part of the National Library of Medicine (NLM) and the National Institutes of Health (NIH).

     To access this huge database, type in any word related to biology. You will get a results page that lists all the publications that contain your word or words. The more words you use, the more specific a response you will get. If you click on the top line that has the authors names in blue, you will usually see an abstract for that publication. Occasionally there will be a large box that is a hyperlink which will take you to an online version of the original paper. The publication of science papers is experiencing a revolution of sorts and some journals allow free access to their articles immediately, others have a delay of 6 - 12 months, some never permit free access. When in doubt, click and find out.

     From the Entrez page for PubMed, you can also search many other databases, In the upper left corner, there is a box that allows you to select other databases (figure 1-3). For example, you can choose to search the literature (PubMed), protein sequences, nucleotide sequences, 3D structures, whole and partial genomes, population sequence sets, OMIM which is a catalog of human health information, taxonomic definitions, and domains which are sequences that are conserved and have well characterized functions. This is the ultimate in one-stop shopping for genomic information. We will use this a lot.

Sample Search of NCBI
     Let's try out a simple search to find a particular nucleotide sequence. Change the search to "Nucleotide", enter the word "clock" and hit the "GO" button. You should get a long list of hits that will cover multiple pages. Now enter the words  "fly clock" .  This should give you a very short list. Find the one for Drosophila and click on the accession number which is a hyperlink. You will see all the information about this particular gene, including the protein and DNA sequences. Now change the search to "clock Drosophila". You should get over 100 hits simply by changing from fly to Drosophila. Perform one last search by entering "period and Drosophila melanogaster". You will still get many hits, even for species that are not flies because they have descriptions that use the words you searched. Scroll down your list until you find a sequence that says:

______________________________________________________________________________

AF251241                                                                      Protein, Related Sequences, Popset, Taxonomy

Drosophila melanogaster period (per) gene, partial cds

 gi|12005687|gb|AF251241.1|AF251241[12005687]

______________________________________________________________________________

The first line has the accession number (AF251241). Below the accession number is line that describes what this hit is. The phrase "partial cds" means this is a partial coding sequence and thus in not complete. On the third line is a list of symbols that tell you a series of other accession numbers that are used in different databases for this particular sequence. On the far left side on the top line are some terms that are also hyperlinks.  Click on the phrase "RelatedSequences" and you should get a short list that includes the full length sequence to the gene called period, or per for short.

Google.com - www.google.com
     If you need to find almost any web page, the best search engine (program that finds URLs and catalogs all relevant key words) is Google. Go to the Google web site and you will see a small box. You may type in as many words as you want (within reason). The more words you enter, the more specific your search will be and Google assumes you want to find pages that include all of these terms, not one or the other. If you know exactly what you are looking for, this is a good approach. If you are just hunting vaguely, start with fewer terms and then add more as you get a sense of what you are looking for.

Sample Search
    Enter the phrase DNA microarray and very quickly you will get over 20,000 hits. You can modify your search and add the term "undergraduate" and see that the list has been reduced about 20 fold. You could use Google to help you find a good summer research job.

Protein DataBase www.rcsb.org/pdb/index.html
     This protein database (PDB) contains all computer files that can show us the three dimensional (3D) shapes of proteins. There are several ways to view these structures, but the easiest is to have the free plug-in called "Chime" which is produced by MDL (Molecular Design Limited)  <http://www.mdlchime.com/chime/>. You will have to register to get your free copy of the plug-in. Once you have logged in, you can follow the links to the download page. It works on both Mac and PC so choose the appropriate one. Once you have installed it, you will need to restart your browser so the new plug-in can become activated.

     Now that you have downloaded the chime plug-in, you are ready to see 3D structures that have file names ending in ".pdb". If you know the PDB file name, you can enter it in the box. If you do not know the PDB ID number, you can use words to search the database (figure 1-4). Using the PDB ID, enter 1AI3, select the "query by PDB id only" box, and click on the "Find a Structure" button. You will see a page that describes isocitrate dehydrogenase (IDH).

     A new browser window will appear. In this window, you will see the amino acid sequence for IDH in the top frame and the structure in the bottom right frame.  Don't rotate the protein yet, leave it in its original position. Click on the button at the left, half way down, that says "Secondary Structure". You will see that the amino acids that make up alpha helices are highlighted in red, beta pleated sheets in blue, and bends in yellow. This has occurred in the amino acid sequence as well as the structure.

     If you place your mouse over any amino acid in the structure diagram, you will see its has been identified in the black window on the top left side, just under the full sequence. This also happens when you mouse over amino acids in the sequence.

     Change from "Secondary Structure" to "Exposure". You will see that amino acids on the surface of the protein are highlighted differently from the rest of the protein. Note the color of the first two amino acids (ME) in the sequence at the top. Using the mouse, find the first amino acid of the protein structure; it is located at the bottom center of the structure frame. Which amino acid is first in the structure?  What happened to the first two amino acids?

    Finally, click on the reset button at the bottom on the left side. Change the color to yellow. Now use your mouse to find the amino acid sequence YICLRPVRYYQ which begins at amino acid 125 and ends at number 135. Click and drag to highlight these 11 amino acids and notice that this portion of the structure has also been highlighted yellow.

     Close the Quick PDB window and you should still have the original page for viewing IDH. Click on "First Glance" and an animated version of IDH should appear. You can choose to turn on and off the different options by clicking on the appropriate boxes.

     Now go back one page and click on the "Protein Explorer" button. Next, make sure your window is properly sized and then click on the button to view 1AI3 from the PDB server. Although it takes a while to load, do not do anything until you see a spinning model of IDH. In the upper right frame, you will see a link that says "Explore 1AI3". Click on this and wait until you see a green box that says ready appear below the structure of IDH. A new set of buttons will appear in the top right frame. Click once on the one that says "water" and most of the red balls will turn to spheres of dots. Click again and they disappear. Click on the other buttons to see what happens.

     Finally, there are a number of people who have collected some wonderful tutorials on particular molecules. If you want to visit some, try these out to see what can be done with chime scripting.

Protein Explorer- http://www.proteinexplorer.org/
This site is maintained by Eric Martz at the University of Massachusetts who has pushed Chime scripting further than anyone else. Martz has tutorials on using Protein Explorer, How to create chime scripts, and has many tutorials for your edification.

Online Molecular Museum - www.clunet.edu/BioDev/omm/gallery.htm
This site is maintained by David Marcey at California Lutheran University. Marcey and his students have created some outstanding tutorials. Click on the link at the bottom of the left side that says "the exhibits".

Nucleic Acid Database atlas - http://ndbserver.Rutgers.edu/NDB/ndb.html
This database contains DNA, RNA, protein-nucleic acid structures. This may be useful if you want to look at non-protein structures.

QuickTime (QT) - http://www.apple.com/quicktime/download/
     QuickTime is a free plug-in that allows you to see movie files. The 15 second biographies that are a part of the online resources for this textbook utilize the QT plug-in. The latest version of QT is 5.x and can be downloaded for Macintosh and PC computers from the Apple web site listed above. Provide the information, choose your platform, and download.

Sample Movie
     To make sure your QT is working, you can check out a 15 second biography <http://bio.davidson.edu/courses/genomics/15secbios/15secbios.html>. Choose your favorite topic and then select a biography to see and hear. You can stop the movie by using the control buttons.

     If the movies do not play properly, then you will need to check your preferences. To do this, choose preferences under the edit menu. Select "Applications" from the list of preferences. You will get a new dialog box; scroll down until you see "MPEG media file" or similar description. Select this line by clicking on it once and then click on the edit button. Make sure the button next to "Plug-in"  has been selected and then make sure the most recent version of QuickTime (5.0.2 or greater) appears in the pop-up menu. If it does not, then you will need to select it by searching through your hard drive and locating QuickTime.

Flash Animations - http://www.macromedia.com/downloads/
     Flash is the software that creates animations for the WWW, TV, movies. It is a very powerful program that is sold by Macromedia. The plug-in is free and you can download it from the site above. You will want to choose the option that says "Macromedia Shockwave Player". Click on this link and follow the directions. It works for PC and Mac, Netscape and IE.

Sample Animation
     There are many good educational animations that use Flash. Some are included with this book. Try out this one that describes how immunoprecipitations are performed. This is used for one case study in Chapter 2 <http://bio.davidson.edu/courses/genomics/IMPfolder/IMP.html>.  This animation includes sounds so if you are viewing this where it is OK to turn up the sound, do so now or use headphones. If you are in a library, you might want to click on the link at the bottom left that will take you to a silent version.

Adobe Acrobat Reader  - http://www.adobe.com/products/acrobat/readstep.html
     Adobe is a software company that makes a program called Acrobat. Acrobat will convert any text file into a ".pdf" format that stands for Portable Document File. Most browsers come with Acrobat Reader free plug-in, but if you cannot read see a PDF file, then you can download it from the page above. Be sure to select the free Reader program and not the full conversion program that costs about $250.

Sample PDF
    Go to PubMed  < www.ncbi.nlm.nih.gov/PubMed/ > and enter these three authors " Evans Skrzynia Burke". You should get one hit entitled "The complexities of predictive genetic testing". Click on the hyperlink of the authors' names and the resulting page has the abstract. Above the title is a box that hyperlinks to the original paper at the journal's web site. Click on the box and you will see an html version of the paper. In the upper right hand corner is a link that says "PDF of this article". Click on this and then click on the "Download" hyperlink that appears in a small box. This box gives you a short citation for the paper and tells you the size of the file you are about to download (217K = 217 kilobytes). Click on the download link and your browser will launch the Acrobat Reader plug-in so you can see the paper as it appeared in the original journal. It is a very good paper if you want to read up on this topic.

     There are many other good research papers that are freely available at PubMed Central <http://www.pubmedcentral.nih.gov/> which is funded by your tax dollars and another set is available at HighWire Press  <http://highwire.stanford.edu/> which is a commercial provider. You can search these two sites for many excellent journals that serve papers in Acrobat format.

Java - platform specific links

Macintosh - http://www.apple.com/java/

PC - http://www.microsoft.com/java/

     As noted above in the definitions, Java is not as universal as it could have been. You will need to got to the appropriate platform link and download the latest Virtual Runtime Machine. Make sure you match your platform, operating system, and virtual runtime machine. Macintoshes tend to work better with IE than Netscape versions 4.7x. As of this writing, Netscape 6.x was still in beta version and was not tested. If you are running a Macintosh on

OS X, you might not have any problems with Java developed by the original standards, or Microsoft standards.

Sample Java
If you go to the SNP Consortium's database, they make nice use of Java. Go to this URL <http://snp.cshl.org/db/snp/snp?name=TSC0019265> and scroll down to the link that says "View Traces": 

     Click on this link and look at the DNA sequences for these particular  single nucleotide polymorphisms. You can click on any of the options and use the scroll bar to view the entire sequence.