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I am in the process of creating a poster for the phage that I recently annotated. The phage is an A4 and the portion of the poster I am working on is analyzing the data that we have collected. I have an excel sheet that has all the Shine Dalgarno scores for each gene that we annotated and decided was the best. Using mathematica I tallied all the data into a table and this is what I got (The x value of the list shows the score, the y value shows the amount of genes that had this score):

How can I create a distribution from this data? Would I need to use a Histogram, a plot, or some other graphic to represent the data?

Biologically speaking, can we make any observations about the genome from these scores?

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you can use histogram to plot this data but I am not sure what your scores mean. In the end your figure should convey some relevant information.. –  WYSIWYG May 12 at 10:07
me either - this print out is highly idiomatic to the software you are using... –  shigeta May 12 at 23:45
Please give us the data in text form so we can work with it. It would be relatively simple to produce a histogram using R for example but I'm not about to copy it by hand. –  terdon May 13 at 15:01
{{441., 6}, {168., 1}, {378., 3}, {483., 8}, {462., 4}, {336., 4}, {143., 1}, {587., 1}, {504., 4}, {819., 1}, {468., 1}, {567., 5}, {351., 1}, {294., 3}, {399., 2}, {438., 1}, {588., 2}, {299., 2}, {525., 3}, {426., 1}, {390., 1}, {609., 4}, {225., 1}, {693., 2}, {420., 5}, {357., 2}, {672., 2}, {231., 1}, {315., 2}, {455., 1}, {252., 1}, {273., 1}, {364., 1}, {300., 2}, {546., 1}} –  indieDev May 14 at 16:14
I know what Shine-Dalgarno sequences are, but what are Shine-Dalgarno scores and how did you determine them? –  5heikki Jul 16 at 15:44

1 Answer 1

I would expect to see if every gene has a strong SDS, and that every strong SDS is in a gene (and if not, an explanation of why).

Mathematically, that can be calculated using Fisher's Exact Test (since I don't see any p-values for your scores).

You should also provide a diagram of the genome showing coding sequences or genes, and mark each SDS on it.

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