User talk:Ksherbina
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Week 1 Feedback
Excellent coverage! (save for creating a new distinct wiki page) Plus, don't forget to email us your concerns and questions.
Items for completion/follow-up:
- Email about worries/concerns/questions/anything else
- Create a new wiki page (beyond your own user page)
—Dondi (talk) 09:45, 3 September 2013 (PDT)
- I have answered your question on my talk page. — Kdahlquist (talk) 10:36, 4 September 2013 (PDT)
Week 1 Follow-Up Feedback
Thank you for sending is the questions/concerns email, and for creating a new wiki page. Moving right along then :)
—Dondi (talk) 17:13, 8 September 2013 (PDT)
Week 2 Feedback
- Thank you for submitting your assignment on time.
- As was discussed in class, you just had one missing amino acid in the -1 frame. For our purposes in this exercise, an open reading frame is simply one without a stop codon.
- Please go ahead and make these corrections on your page to earn back the points you missed.
- The Nirenberg article was written as a memoir to other practicing biochemists, so it was dense. I hope you enjoyed it anyway!
— Kdahlquist (talk) 15:08, 11 September 2013 (PDT)
P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:19, 12 September 2013 (PDT)
Week 3 Feedback
- Thank you for submitting your assignment on time!
- Good to hear that you succeeded in exerting control of your file extensions.
- Your sed and match skills are great! All of your commands were correct.
- For the third match question, you missed that the command was supposed to have run on the hs_ref_GRCh37_chr19.fa file, not 493.P_falciparum.xml. The commands were still successful and you made the correct inference about how match and grep/wc are different, but you were using different data from what was specified.
- Thank you for providing a complete set of links across your user page, assignment page, shared journal page, and individual journal answer page. These really help us to get around from one page to another. The tabular arrangement makes things easy to spot as well.
—Dondi (talk) 22:34, 14 September 2013 (PDT)
Week 4 Feedback
Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
- -35 box was correctly identified with an appropriate command.
- -10 box was correctly identified with an appropriate command.
- The transcription start site was off by one base.
- Ribosome binding site was correctly identified with an appropriate command.
- Start codon was correctly identified with an appropriate command.
- Stop codon was correctly identified with an appropriate command.
- You missed that the terminator includes 4 additional base pairs after the hairpin.
- The mRNA strand is short—only the start-to-stop codon was identified, but transcription actually goes from the transcription start site to the end of the terminator.
- You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there—keep it up!
Let me know if you have any questions.
—Dondi (talk) 23:16, 24 September 2013 (PDT)
Makeup Point Update
You have been credited for making the following change(s) to a prior assignment:
- Your Week 4 wiki comments now have the correct code for locating the transcription start site.
- Your Week 4 wiki comments now have the correct code for marking up the complete terminator signal.
- Your Week 4 wiki comments now have the correct code for computing the complete mRNA strand. The revised command skips the substitution of t for u, but because this was in the original command, the correction is interpreted as needing to address only the proper start and end of transcription.
- Regarding your question about why 1,3D did not work as expected, note here that “1,3” represents an inclusive range—i.e., lines 1 to 3. I understand how the comma threw you off—in many other systems, the comma indicates individual choice. In sed, however, it indicates a range.
If you have any further questions, let me know. Thank you!
