Homework #0: Adopt-a-Prokaryote
CSE 427: Computational Biology
January 5, 2009
For some of the 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 796)+1.
-
Go to the course
wiki. You'll find a numbered list of 796 completely 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 nor the words "Taken" nor "Community Prokaryote"
appears on that line in the wiki.
- Your prokaryote appears on the NCBI Microbial
Genome page. (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. There may be
some slight differences in wording, which is fine, such as
"Francisella_tularensis_FSC_198" on the wiki and "Francisella
tularensis subsp. tularensis FSC198" on the NCBI Microbial
Genome page.)
- 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, select the Edit tab on the wiki's
prokaryote list, type your name in the obvious place (being careful
not to edit anything else on this community page), and click "Save
Page" at the bottom of the page. (You may need to use the outer
scroll bar to find that button.) Make sure your name now appears in
the last column next to your very own prokaryote. Congratulations!
You've adopted a healthy new one-celled organism.