NCBI Workshop Comments and Questions Spring 2008

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Please use this page to ask questions or post notes about the NCBI assignment.--Dr. Byrne 10:37, 23 January 2008 (EST)--Dr. Byrne 10:37, 23 January 2008 (EST)

i tried to solve the first question again used the flow chart provided but i could not follow it. NCBI Homepage -> TaxBrowser -> (i was stuck at this point)Homo sapiens -> Entrez Gene -> Search for “beta globin” -> click “Reference Sequences” in Table of Contents

i went to NCBI home page - clicked tax browser then what should i do.. --nimish 00:40, 28 January 2008 (EST)

• Let's put all questions on the "article" tab, not the "discussion" tab. I've copied your question over to that page and will try to answer it there. --Dr. Byrne 10:55, 28 January 2008 (EST)

On the TaxBrowser page you can either type Homo sapiens in the box or click on the link:

--Dr. Byrne 10:55, 28 January 2008 (EST)

I am doing all these exercise step by step for example exercise 2 I went and filter for RefSeq. The information that I receive there what do I do with it? copy paste on WebCT? or Copy the link on WebCT? Are we going to follow for other exercises?--Patels19 16:57, 28 January 2008 (EST)

• The question reads: "What nucleotide constitutes the first nucleotide of the start codon in the RefSeq mRNA in the human beta hemoglobin?" In the box, describe the series of pages you used to navigate to the page with the answer and then what characteristic on that page tells you where the start codon might be. --Dr. Byrne 10:28, 29 January 2008 (EST)

I can't find the first nucleotide for the start codon.. i found something that says origin with a bunch of nucleotides that follow it but i'm not sure if that is the proper section i should be looking for.

• It looks like Christina asked this question but then Nimish did some editing apparently asking and then removing some questions as he solved them himself. Good idea to sign your questions and, if you solve your own questions, just answer them on the page to help other people! But to the point of this question, in the exercise, there's a link to an interactive page at NCBI that demonstrates the nature of the NCBI nucleotide record. There you should see an abbreviation in the Features table that will indicate the Start Codon. --Dr. Byrne 10:33, 29 January 2008 (EST)

also for the question involving the number of exons i found sections labeled exon with a number next to it but i'm not sure if that is the actual number of exons or not. any suggestions?

• A second question from Christina, I think; There are a number of different resources to get the exon structure of a gene. I'd accept any one of them, just let me know the set of pages you went through to get to your answer. Geeks refer to that pathway of pages as breadcrumbs, referring, I think, to an old English/German fairy tale about two children who thought they could find their way out of the woods by leaving a trail of bread crumbs... but the birds, sadly, ate them up. --Dr. Byrne 10:28, 29 January 2008 (EST)

  A question was posted here on 2/16 regarding the EMBOSS Suite.  I've move that question to the EMBOSS Suite Spring 2008 article.  --Dr. Byrne 12:45, 17 February 2008 (EST)