EMBOSS Suite Spring 2008

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Please use this page to discuss and/or ask questions about the EMBOSS Suite assignment. --Dr. Byrne 14:32, 6 February 2008 (EST)

I have question about EMBOSS assignment. In the questions # 22 and 23 where we are asked to use patmatmotifs and pscan applications I constantly get an error. I entered protein seq. and run the application and pscan give me Error application terminated

  EMBOSS An error in embmat.c at line 123:

prints.mat file not found. Create it with printsextract. message and patmatmotif gave the following message Error application terminated

  EMBOSS An error in patmatmotifs.c at line 101:

Either EMBOSS_DATA undefined or PROSEXTRACT needs running --Ryan 12:02, 22 February 2008 (EST)I don't know what I did wrong. The protein seq is correct I compared my EMBOSS generated seq with NCBI database they are the same. So may be I should change some defoult parameters of my request? -- User Khakhina/Svetlana Khakhina 14:28, 16 February 2008 (EST)

  Oops. The server was updated and it looks like there are some issues. I will notify tech support.  Sorry for the 
  inconvenience.  --Dr. Byrne 12:47, 17 February 2008 (EST)
  The technical problem has been resolved. I also noticed a typo in the original posting.  I asked you to use an application called 
  "patmotifs."  That doesn't exist.  The name of the application for question #22 is "patmatmotifs."  I've now corrected it in the 
  WebCT document.  --Dr. Byrne 21:46, 17 February 2008 (EST)

Is there a question for number 8? looks like it's just a statement and doesn't require an answer--Christina 19:49, 19 February 2008 (EST)

  That could be the case.  Some of them are just observations.  --Ryan 12:02, 22 February 2008 (EST)

For Human genomic Sequence I am Using the following sequence with the Accession # NC_000011.8 (the one in the work shop HS_11) is it right or I am supposed to use NG_000007.3

  Please use the sequences that I am providing you as links from the workshop--Dr. Byrne 17:48, 24 February 2008 (EST)

which is under Genomic in Entrez Gene (Pubmed). Because when I use "needle" for Human mRNA with NC_000011.8 vs. Human mRNA with NG_000007.3 gives me two different answers for how many regions are aligned. Also, what do you mean when you ask 11) What do you think each region approximates?Thank You.--Patels19 16:48, 20 February 2008 (EST)

  Ryan's put you on track in his help, below...
  I'm asking you to think about why you get that pattern, matching mRNA against a 
   genomic sequence.  Think biology. --Dr. Byrne 17:48, 24 February 2008 (EST)

   NC_000011 is chromosome 11 for human.  NG_000007 is a mRNA.  If you align a mRNA sequence to 
   a genomic sequence, what does that tell you?  Don't think about the specifics of the sequences 
   themselves, but more high level.  --Ryan 12:02, 22 February 2008 (EST)
  

I was doing the EMboss assignment and i'm a little stuck on #25 regarding the similarity value? I'm not sure what that number is. Is that the same as plurality number??--Phuong 18:35, 21 February 2008 (EST)

  When you do alignments, the results pages contain two statistics, "Similarity" and "Identity."  In the case of comparing
  two nucleic acid sequences, you'll see the two values are identical.  When you compare two amino acid sequences, the values
  are likely not identical.  What is going on?  --Dr. Byrne 17:48, 24 February 2008 (EST)

    Dr. Byrne is away this weekend and will reply to your questions next week.  If someone else in the class 
    can offer an answer to this, please post it here.  --Ryan 12:02, 22 February 2008 (EST)

  I am sill out of town and will not have much time for anything before class on Wednesday.  --Dr. Byrne 17:48, 24 February 2008 (EST)