Talk:CH391L/S14/Ancestral sequence


 * --Ella Watkins (talk) 13:42, 12 February 2014 (CST) Are there programs online that can be used to apply the "Methods of inferring"? Like BLAST? If so, it might be good to add what some of those programs are. Also I know there are 2 ways of citing, but it appears to me that the more popular way is to cite according to what comes first, second etc. Maybe reconsider how you cited so that you can put number hyperlinks at the end of all of your sites.


 * --Dennis Mishler (talk) 14:20, 13 February 2014 (CST) Cindy, the second figure does not display. You may need to upload the figure again.
 * Ajv684 (talk) 18:26, 13 February 2014 (CST)This is a very comprehensive wiki, I like the way the topic was developed by starting with a brief overview and then going on explaining different approaches to obtain ancestral sequences to finally explain some concrete examples. However, I believe that presenting a comparison table to explain differences in the different approaches to derive ancestral sequences would be of great help. All those methods look very complicated to understand for a lay reader so I would as well suggest explaining the most popular one by using a figure/scheme/flow chart so that it helps making it more clear. Overall, very good wiki.


 * --Liz (talk) 23:39, 13 February 2014 (CST) Lots of good information on an interesting topic here. I like the intro and history sections. Reading the Pipeline, which I think is a good way to introduce the technique, first thing is - I don't know what maximum likelihood is yet.  And would it be better to say "ancestral gene sequence is inferred."  You might want to add a section about the programs used to align sequences.  I know it's trivial but you have a separate section for each of the other pipeline steps. Under the Methods, the limitation of Consensus Sequence should be two sentences? Why does it matter that phylogenetic relationships are ignored? You talk about the relationship between extant species used for all the methods- maybe at the top introduce why this matters. For the figure, I understand that you are illustrating the methods coming to different conclusions, but I'm not sure how you got there. What about that figure shows how you came to different conclusions based on the inference method? I really like the example of the coral.  (lower wavelengths = longer wavelengths?) Did the paper give any insight into why a change in color might have helped the coral? (maybe outside the scope of this page- just wondering).  Would be nice to upfront define all the classes of coral colors you name, that way when you show how it has evolved we know physically what that means. Not sure I would call the red more specific though...that means something else to me. Anyway that's definitely enough from me.  Good job!


 * --Jordan Monk (talk) 03:15, 14 February 2014 (CST) I feel like your wiki could benefit from a simple phylogeny figure showing the ancestral states and base changes across multiple generations, which might make some of the methods descriptions easier to digest. Overall, good presentation and I think the content selections were very appropriate for the topic.


 * --Gabriel Suarez (talk) 06:21, 14 February 2014 (CST) Wow, reconstruction of genes from more than 1 billion years ago? Where/which is the citation? I was interested in knowing more! Third sentence, in the Coral section, "was not fully understand", I think you meant "understood". When you cite, it common to proceed: Brigham et al.(year)computed...that way looks better than Brigham "et. al" computed... Structure is good and good info!

--drewtack (talk) 20:12, 16 February 2014 (CST)You have a collection of examples, maybe you should format these in some manner, and put them under a common heading. It could hedge up the style a little, right now it looks like each of those examples is a major topic in the wiki, when I would probably consider them subtopics of a major section of examples.


 * --Chen-Hsun Tsai (talk) 08:51, 14 February 2014 (CST) I think the overall content and structure is very informative and organized. A minor point is there is just one figure. Maybe you can put some of the figures or charts that you use in the presentation to make the wiki easier to read and understand.

--Dennis Mishler (talk) 08:28, 14 February 2014 (CST) Alex's Critique Overall Format and structure: Overall, the page was well organized and well written. The concepts presented were very useful for exploring the topic, and helped underline the idea very well. The multiple examples in particular helped show the variety of ways this has been used quite effectively. Other than a few minor typos and errors (failed citation in history section where it says Thornton, second picture not linking, glutocortocoid recepot instead of receptor in the steroid hormone receptors section), the grammer and punctuation were fine.

Introduction and background material: The introduction explained what ancestral sequence reconstruction was very clearly and concisely. While brief, it does a good job of summing it all up. The history section had good points in time to use, though some elaboration on the advancements or techniques mentioned in the 2000s today may help the reader understand how ancestral sequence reconstruction is done today.

Methods and main body/concepts: The methods section is useful, though a bit more explanation of what the phylogenetic uncertainty mentioned in the BMCMC method, and perhaps how the branch length (number of substitutions per site) affects the results. The examples are very well done, showing clearly what the technique is used for and how it can work in real situations.

Relation to iGEM and future directions: While there is no mention of iGEM, that's not strictly necessary. The future directions section does a good job of introducing new ideas that the method is being discussed in, as well as the possible benefits of those ideas, in a very clear way. One thing that may be nice if possible is some ideas or techniques that people are discussing to make ancestral sequence reconstruction easier or more accurate.

Figures, Figure legends, and citations: The figure that does work is very useful in underlining the differences between the two methods discussed. However, the second figure is not linked properly and does not appear on the page. The citations are mostly done correctly, with a couple points to mention: there is a part in the history section where it says (Thornton), which may or may not have been intended to be a citation. Also, while a couple of the references do have the short blurb about them, not all of them do.


 * --User:Ashley Kessel (talk) 06:23, 14 February 2014 (CST) Great article, a few of the paragraphs do not have any citations in them (although the same ideas are cited later paper). For clarification sake I recommend putting the citation in those paragraphs as well.