EMBOSS Workshop

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Please ask questions or make comments about the EMBOSS assignment and workshop on this article, below. For this question:

Use patmatmotifs to search for known motifs PDGF-R.

(17) What is/are the motif(s) found and location(s)?

Do you want PDGF-R alpha or beta?--Michelle P 22:07, 25 September 2007 (EDT)

  • You can link to the sequence we're interested in from the exercise page That's the beta precursor I've chosen.

Will we also be handing in this assignment through SAIKI?--Michelle P 16:06, 3 October 2007 (EDT)

  • Yes. Click on the "Assignments" link in the mercury site. --Bruce 10:18, 4 October 2007 (EDT)

I went to submit my EMBOSS assignment through SAKAI, but I do not see the link in the mercury site under assignment. All i see is the NCBI assignment. Am i not looking in the correct place or am I doing something wrong?--Michelle P 12:19, 5 October 2007 (EDT)

  • Sorry, the tool is up there now. I've given it an extra day to make up for it! --Bruce 13:03, 5 October 2007 (EDT)

Does anyone have any good resources to steer me in the right direction for question 10 (Do you think that this program has given you exact biological alignment of the mRNA on to the genomic DNA?)? I don't understand the hints given here... --Cukierwj 13:10, 5 October 2007 (EDT)

  • Think about, or look up, exactly what a splice site consists of. Then ask what this computer program is able to do or is considering in the alignment. It's one of those thinkaboutit questions...--Bruce 14:09, 5 October 2007 (EDT)

How to delete the uploaded assignment in Sakai? Or we don't have the access to do that? --yuan 17:38, 5 October 2007 (EDT)

  • Never thought about that! I'll need to check, but cannot at this point. Just email the correct assignment to me. --Bruce 17:23, 6 October 2007 (EDT)

The deadline for the EMBOSS assignment posted here on the WIKI page is October 8. I noticed just now that the link on SAKAI is up, so I uploaded it. I've had it ready for ages now, and apparently I am submitting it late? The SAKAI has the deadline Oct 6. --Lukacsvi 21:58, 6 October 2007 (EDT)

  • My error; I was late getting the saki functioning, so I extended the deadlines. You're fine. --Bruce 13:39, 7 October 2007 (EDT)
  • Thanks, I'll check it more often in the future. --Lukacsvi 14:03, 7 October 2007 (EDT)

Sorry I did not know where to put questions for the blast assignment. I am having much difficulty with it because the site has changed. I am assuming nr database means the rat data base. Also, the conserve domain picture I can not find. I think the BLAST does not have that feature anymore. I remember it on the old BLAST site because I use to use that feature. However, I cannot find it on the new BLAST site. Can you help me with this?--Michelle P 11:15, 8 October 2007 (EDT)

  • Try doing a protein blast with no species specification with the human query sequence. nr stands for non-redundant, so under the protein blast select "non redundant protein sequences" as database, the results should display conserved domains! (at least it did for me) --Lukacsvi 15:33, 9 October 2007 (EDT)
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