CS177 homework assigned March 2

1
CS177 homework assigned March 2

• this can be either a group or individual
  assignment, whichever is easier for you
• this will cover
• multiple alignment
• html and java
• this is a lot of stuff, so it is due in 2 weeks
• the balance should start shifting from assigned
  homework to doing your projects

2
vertical multiple alignment

• pick a gene, find the human mRNA (ie, NM_XXXX)
  RefSeq, and query NCBI nucleotides using BLAST
• see if you get hits to 5 or 6 different species
• if not, try another gene
• pick out one good hit (ie, low p value and pretty
  long) for each species (including the original
  human RefSeq)
• submit these sequences to clustalw
• visually identify one column on the alignment
  that exemplifies highly conserved, one for
  moderately conserved, and one for poorly
  conserved

3
horizontal multiple alignment

• go to pfam site
• http//www.sanger.ac.uk/Software/Pfam/
• look it over until you are completely confused
• here is my example
• run through it
• then do your own example
• enter fibrin in keywords box
• click on kringle
• click on view species tree
• click in box next to homo sapiens and then click
  view selected species alignment
• meditate on what you are seeing
• amino acids, not nucleotides
• uses the one letter symbol format for amino acids
• can you make any observations about the multiple
  alignments?
• try it in a second browser window for gorilla and
  compare with human
• ditto for mouse

4
java

• take a look at the NCBI_STRUCTURES.java program
• go to the web site from the last homework
• http//java.sun.com/j2se/1.3/docs/api/index.html
• see if you can find something in the web site
  that helps you make sense out of one or two
  things in the NCBI_STRUCTURES.java program
• hint Look at the URLConnection class
• just spend 30 or 40 minutes on this. dont get
  too frustrated now - you will have plenty of time
  for that once you get a real job
• think of this as a growth experience that builds
  character

5
java and html - we will do this in class next
week, but you will have to do it on your own also

• the NCBI_STRUCTURES.java program can be used as a
  prototype for this part
• go to NCBI web site
• view the html source code underlying the web
  page
• locate the form action POST stuff
• look at the stuff that happens between the ltform
  and the lt/form tags
• copy the html source into a file, and change POST
  to GET, save as NCBI.html
• open another browser window, and read in
  NCBI.html using the File menu
• perform a query type of your choice
• this will not actually work since POST is
  expected, but notice the stuff in the URL window
  that is exposed by using GET
• copy the html source into a file, and change the
  NCBI URL into the URL for my cgi program
  testloop.cgi, save as NCBIecho.html
• repeat the last 3 steps, and see if the echo is
  the same as the GET
• modify NCBI_STRUCTURES.java
• make it put out what you need for your query
• modify the part that does the parsing (ie, the
  line with ltddgt) to make it relevant for parsing
  your output
• hint figure out the modification by looking at
  the real output html source from a real query at
  the real NCBI site
• if you cannot figure out how to modify the
  parsing, then at least comment it out entirely
  or you will not see any output!!
• remember that the java program is run as
• java NCBI_STRUCTURES inputfilename
• inputfilename is the name of the input file that
  has 4or 5 gene names to test oout