Name:  


Exercise 5
STA 4953 (Spring 2001)


Starting Netscape
If your are working from a SUN station, log on to helix and set up the environment for X-windows display. Then type "netscape &" to the helix prompt. If you are working from a PC, click on the Netscape icon.
 
Retrieving a sequence from GenBank (the United States nucleotide and protein sequence database maintained by the NIH).

  1. From our main Bioinformatics page, follow the "Databases" link to GenBank. Read the paragraph, "What is GenBank?"
      a) How many bases and how many sequences are contained in the current version of GenBank?
      Bases:
      Sequences:
      b) What are the names of the European and Asian counterparts of GenBank?
      European:
      Asian:
      c) Which component of the NIH maintains GenBank?
  2. Click on the "Entrez" link near the top of the page. Follow the "About Entrez" link to get an overview of this sequence retrieval system. Go through the tutorial. What sequences have you retrieved during the tutorial?
  3. Now can you try to find all sequences related to hemoglobin in humans (homo sapiens)? How many sequences do you get in your search results?
  4. Sequences can be found much more quickly if you know their accession number in GenBank. Try retrieving the following four sequences by typing in their accession numbers (given in parentheses) to Entrez, view the text display in the GenBank format, and save them on Helix:
      Homo sapiens hemoglobin alpha 1 chain (NM_000558)
      Homo sapiens hemoglobin alpha 2 chain (NM_000517)
      Homo sapiens hemoglobin beta chain (NM_000518)
      Homo sapiens hemoglobin delta chain (NM_000519)
    [Note: If you are working from the PC's, you'll need to save these sequence files to the PC first, and then upload them to Helix with start>programs>ws_ftp.]
  5. From each of the four GenBank sequence records, use a text editor to make a copy of the nucleic acid sequence only and put it in a *.na file. Also copy the amino acid sequence and put it in a *.aa file. [Note: If you are working from the PC's, it is easier if you do the text editing with notepad on the PC and then upload the edited files to Helix.]
  6. Put all the files you made in this exercise in your ex5a subdirectory. Write down their file names in the table below.

    7. Directory path   
    ************ Alpha 1 chain Alpha 2 chain Beta chain Delta chain
    GenBank file
    Nucleotide seq
    Amino acid seq

  7. Look up from biological literature (e.g., biological links on our web site, biology textbooks, dictionaries, encyclopedia) about hemoglobin. Answer the following questions.
      a) What is the biological function of hemoglobin?

      b) Which cells in our body contain hemoglobin?
      c) How many chains of amino acid is a hemoglobin molecule composed of?

      d) Which human chromosomes contain genes for making hemoglobin?