Homework #0: Adopt-a-Prokaryote
CSE 427: Computational Biology
January 8, 2013
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 2207)+1.
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Go to the numbered list of 2207 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
Genome list and its "Status" shows as a filled in circle, meaning
completed. (Search for the full name: many species have a number of
different strains in these tables, such as Bacillus cereus ATCC
10987, Bacillus cereus ATCC 14579, Bacillus cereus E33L. Be sure
you click through until you can see the Genome Sequencing Project
table for your particular strain. You may have to click on the "See
more ..." link below the Genome Sequencing Project table in order to
find your strain. The Genome Sequencing Project table for your strain
will show the "Status" plus other useful information you will need
later, such as the size, GC%, number of genes, and number of proteins,
so you may want to bookmark it once you find it. There may be some
slight differences in wording, which is fine, such as "Francisella
tularensis FSC198" 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 TA with the full name of your
prokaryote.
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Congratulations!
You've adopted a healthy new one-celled organism.