Homework #0: Adopt-a-Prokaryote
CSE 427: Computational Biology
January 3, 2011
For some of the homework assignments 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:
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Let I be your student ID number. Compute h(I) = (I mod 1232)+1.
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Go to the numbered list of 1232 completely
sequenced prokaryotes. Look for the line numbered h(I). This
gives your tentatively assigned prokaryote.
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Does your prokaryote pass all of the following tests?
- Your prokaryote's entry in the numbered list does not say "Taken"
or "Community prokaryote".
- 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" in the numbered list 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, at least one .faa 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.)
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Send mail to the instructor with the name of your
prokaryote.
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Congratulations!
You've adopted a healthy new one-celled organism.