Ryan N. Willhite Week 8

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Week 8 Assignment Page

Chapters 2-4

  • www.expasy.org/sprot
  • takes you to exPASy proteomics server
  • dUTPase coli type in
  • changed drope menu but intial is right one
  • However not 3 proteins but 5 pages worth
  • accession P06968 found on fourth page of the five
  • once clikcing the accession number of the protein, the sequences were lower on the page
  • There are more categories as well on this page of information about the protein
  • could not find advanced search however categories shown n screen shot in bioinformatics for dummies are seen in the drop down menu of the search engine

  • no advanced search so could not deselect trEMBL box
  • typed in dUTPase again
  • over 3000 proteind came up instead of the 211 that was said in the book
  • selected most of these sequences and not all into one format
  • selected all from the first page
  • (Insert screenshot)
  • the word that is supposed to be there in french is not there anymore, it is retrieve
  • after retrieving we did not have to copy and paste all sequences on one file simply because they were alredy there in several formats instead of just txt like they mention in the book.
  • Therefore, on page 50, it is already done for you and not a hassle at all
  • (insert snapshot)
  • search query: "HIV Gp120" make sure to go to drop down menu and hit reviewed- yes
  • gp160 will show up chose second
    • (P03377)

Chapters 5-6

  • ch 5
    • www.ncbi.nlm.nih.gov/gorf/gorf.html
  • copied sequence
  • clicked orfind button
  • ch6
    • www.expasy.org/tools/#primary
  • a bit harder to find ProtParam because it was not exactly where they said it would be
  • click compute parameters button
  • analysis
  • Running protscale
    • www.expasy.org/cgi-bin/protscale.pl
  • accession number
  • range of analysis
  • Results from TMHMM