Homework #0: Adopt-a-Prokaryote
CSE 490C: Computational Biology
March 28, 2006
For the first few homeworks, you are going to need your very own
prokaryote. You will each hash yourself into the table of sequenced
prokaryotes, in order to find yours. Here are the details:
-
Let I be your student ID number. Compute h(I) = (I mod 317)+1.
-
Go to the course
wiki. You'll find a numbered list of the 317 currently sequenced
prokaryotes there. Look for the line numbered h(I). This gives your
tentatively assigned prokaryote.
-
Does your prokaryote pass all of the following tests?
- No student's name appears on that line in the wiki.
- Go to the MicroFootPrinter
species list. Enter one of the words from the prokaryote's name
in the Search box and click "Search". Your prokaryote's name should
appear in the resulting list, in at least one line not containing the
word "plasmid". (Check the full name: some species have a number of
different strains in these tables, such as Bacillus cereus ATCC 10987,
Bacillus cereus ATCC 14579, Bacillus cereus E33L.)
- Your prokaryote appears on the NCBI Microbial
Genome page. (Check the full name again.)
- Find your prokaryote on the NCBI Microbial FTP
page and click on its link. That directory should have at least
one .fna file and at least one .ptt file. At least one of the .fna
files should have size at least 800 KB as listed in the directory.
If your prokaryote fails any of these tests, go back to step 1 using
instead h(2I), h(3I), ... (I actually expect that almost everyone's
first choice will have worked. If your first 3 choices don't work, or
you encounter some other problem,
send mail to the instructor explaining what's happening.)
-
Enter your name in the course wiki next to your prokaryote, which now
belongs to you. To do this, you'll have to click Create an Account
in the upper right. Once you've created an account, select the Edit tab on the
wiki's prokaryote list, type your name in the obvious place, and click
"Save Page" at the bottom of the page. (You may need to use the outer
scroll bar to find that button.) Be careful not to edit anything else
on this community page.