Talk:Inverted repeat

Not true

"When no nucleotides intervene between the sequence and its downstream complement, it is called a palindrome." — Preceding unsigned comment added by 129.241.132.131 (talk) 15:26, 18 October 2011 (UTC)

Well, it turns out that a word is left out of this statement. It should say "...its downstream reverse complement..." With this update, the statement becomes true. Please see the updated article for an example. If you should still feel differently, please provide an example where the statement is false.

-- Jim Perry (Jim892) (talk) 17:31, 29 October 2013 (UTC)

OPEN NOTICE to anyone interested in this page - Suggested Improvements

Hello! As part of our Molecular Biology course at Johns Hopkins University we (Jim Perry and Godwin Ifere) will be working to improve this article. Here is a summary of our suggested improvements and we would like your input and suggestions!

We plan to define the term and give examples and then show some specific areas were Inverted Repeats have importance. Ideas so far are:

• Inverted repeats play a significant role in determining specific traits in humans, including its heavy presence in the Y chromosomes, within genes important for male fertility.
• Terminal inverted repeats flank the ends of many transposable elements, signifying their importance in various mutations.
• Because inverted repeats play a role in both DNA and RNA, we might discuss the effects under two major divisions for the article.
• There are existing database of Inverted Repeats and some are listed in the current article as external links. We will likely investigate these and document there general areas of coverage in the article.

-- Jim Perry (Jim892) (talk) 18:07, 19 October 2013 (UTC)

Use this link to see our detailed outline for the "future state" of this article: User:Jim892/sandbox2 —Preceding undated comment added 02:58, 23 October 2013 (UTC)

Unit 8 Discussion on article - Molecular Biology Group Project

Hello Godwin. I put the basic structure in place on the Inverted Repeat article. I'm going to work on the "Understanding Inverted Repeats" section with some self-made illustrations. Could you write something for one (just one for this week) of the sub-items under "Biological Features and Functionality" for the Unit 8 work? And, could you also take a shot at improving the opening explanation? (We need to expand to 1 to 3 sentences to show how the topic has merit. I'm thinking that the initial sentence that gives a referenced definition can stay "as is". In future weeks, we will do the remaining sub-items under "Biological Features" during Unit 10, 12 and 14 (when we make the 2nd, 3rd and final contributions to the article). Also, feel free to change the wording of the sub-items under "Biological Features and Functionality" if you wish. Regards, Jim Perry (Jim892) (talk) 18:01, 28 October 2013 (UTC)

Introduction

Hello Jim,

I have submitted my write up on the introduction to Turnitin. I am waiting for it to be approved, so that I can move it on to our page this afternoon. I will certainly continue to work on the sub-item "Biological features and functionality" today. I'll keep working. Let's keep in touch. Godwin Ifere 17:13, 29 October 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Sounds good. I changed the first sentence to improve on the "definition" because the old wording just didn't really do the job completely. Let me know if you think it is ok. So my thinking is to have you add your introductory information starting with a new paragraph just after the sentence that says "Likewise, a palindrome is ... with no intervening sequence". Feel free to remove the two sentences that are right after that (or perhaps you have already incorporated them in the new introduction). I'll take care of writing the "unit 8 progress report" on the group page by midnight tonight. Regards, --Jim Perry (Jim892) (talk) 19:28, 29 October 2013 (UTC)

Comments from Pozmi

Since inverted repeats were near the top of my topic preferences list I had become fairly familiar with the previous page. Clicking on the page today I could already see big changes and the framework you've laid down for future edits. From what little content was on the original page, I see you've already addressed the largest issue: the "not true" that was declared on the talk page. With the page being live, accuracy is a top factor and I appreciate that you edited the material that was already there instead of just adding to it.

Writing Organization: In fitting to Wikipedia standards, one point I would like to mention is your subheadings. There are some subheadings, for example under the section "Biological Features and Functionality", that are currently empty. It is clear that you will be adding to these, but usually pages don't include empty headings. Since all of your future sections are included in the article outline in your sandbox, I would suggest including more headings as you add material. This way the live version of the page will have a consistently "finished" look.

Content Coverage: In regards to the article's tone, it is unbiased and clear. There is plenty relevant terminology but not unnecessary jargon. Although this topic requires comprehension of a number of other topics, I believe it's started at a good level to introduce the topic. I particularly like the step-by-step approach when comparing different motifs. Wikipedia's style guide generally refrains from using the first or second person POV except in quotations, so I would suggest rephrasing instances of "we" and "you" and remove the "please" in "Please see the 'Biological Features and Functionality' section below for more examples." For another article that uses "see below" check out Synesthesia. In that case, they directly link the word "below" to the section they wish to direct the user to.

Wikilinking: Perhaps you could add a few more internal links to some of the terms mentioned in the lead section, like exons, introns, and microsatellites.

Referencing: The current content is well-cited. There is an in-line citation every few sentences in the lead section and your references include textbooks and articles -- all verified sources and no original research. Some of the later sections include blocks of quotes, but I imagine summaries and explanations will be included in due time.

Illustrations: Along with your written edits, I see you've already added one of your own images. This is a great contribution that other Wikipedians can make use of as well as as well as other internet users under the correct terms. Both this image and the text representations are visually helpful to understanding inverted repeats.

I think the outline in your sandbox will lead to a very comprehensive article. I especially look forward to the sections on the significance of inverted repeats and different databases (which are an excellent resource to provide). Great start! --Pozmi (talk) 20:45, 4 November 2013 (UTC)

Hi Pozmi. Thanks for all the good feedback and suggestions. We will go to work and update per your suggestions. Regards --Jim Perry (Jim892) (talk) 22:59, 4 November 2013 (UTC)

Hi Pozmi, You comments indicate that you took time to go over the whole article, including our compliance with Wikipedia style. As Jim Indicated we have taken note of your comments and suggestions, and would surely make the necessary corrections and adjustments. I have taken particular note of your suggestion for the addition of links to certain terms already present in other Wikipedia articles. Accept our thanks again.Godwin Ifere 05:32, 12 November 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hello again Pozmi, I liked your suggestion about adding links to phrases like "see below" such that the link takes the reader directly to that section. We now have these added to the article in the places you suggested and will be on the outlook for more. Thanks for the great idea! -- Jim Perry (Jim892) (talk) 14:48, 12 November 2013 (UTC)

Hello Jim and Godwin, nice progress in the past weeks! Along with adding another image, I see that you're very skilled at formatting -- including the image size, image placement, and caption. In fact, after looking at your code I'll be changing the image formatting for my own page!

I think your introduction starts strong with ample wikilinking and inline citations. I'm glad that some of my previous suggestions were helpful. I especially like the "Programs and Databases for Inverted Repeats" section. Full of wikilinks, diverse resources, and enough description to help users know what each database offers.

For the "Location of inverted repeats in the genome - how, why and where[edit]" subsection, I see that it is currently just a quotation. I would suggest taking out "how, why and where" from the subsection title, and breaking apart the quotation to add in explanations of how, why, and where throughout the paragraph.

Nice work and looking forward to the rest of the article! --Pinar --Pozmi (talk) 03:02, 23 November 2013 (UTC)

Article's looking great! I like the use of colour to display the 5'-3' and 3'-5' sequences. A suggestion: add in 5' and 3' to the sequences in the "Palindrome vs. inverted repeat" section so that all the sequences are in the same format throughout the article. As well, moving "5'-TTACGnnnnnnTTACG-3'" down to the next line in the "Direct repeat vs. inverted repeat" might make it easier to see with the whole sequence in one line. --Pozmi (talk) 21:44, 7 December 2013 (UTC)

Hi Pozmi. Thanks for the suggestions. I just made the updates per your suggestions. Regards, --Jim Perry (Jim892) (talk) 22:06, 7 December 2013 (UTC)

Comments from Madscientist2007

Congratulations on your first contribution to your article “Inverted Repeats.” You both obviously put a good deal of time into laying down the structure for your article as evidenced by your article selection rationale and the discussion on the article’s talk page.

While this is only your first contribution, your headings and subheadings provide a logical and well thought out framework for your article. They also lend themselves well to further subdivisions. I noticed that many of your subheadings still need to be filled in, which is understandable , as this article is a work in progress. You mentioned in several of your discussions that inverted repeats come into play with both DNA and RNA and that you plan on addressing this. I think that this great thing to keep in mind as you continue your work. This is especially pertinent for your blank sections, especially if major distinctions exist between inverted repeats in DNA and RNA. You may even want to break some of your subheadings down further based this. For instance, in your subsection entitled, “Most common biological functions using Inverted Repeats,” what functions are attributed to each type of nucleic acid? Even if you do not use subheadings, I would make any distinctions clear in your text.

Following a similar train of thought regarding your sections, you provide a great deal of pertinent information in your introduction section. However, I wonder as to whether some readers might this section overwhelming. I am not suggesting that you should eliminate information from your introduction, but some of it might be better placed elsewhere. For instance, your introduction might flow better if you presented it somewhere along these lines:

“An inverted repeat (or IR) is a sequence of nucleotides followed downstream by its reverse complement.[1] The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. When the intervening length is zero, the composite sequence is a palindromic sequence. (See examples below.) Inverted repeats have a number of important biological functions. They define the boundaries in transposons and indicate regions capable of self-complementary base pairing (regions within a single sequence which can base pair with each other). See "Biological Features and Functionality" section below for more examples.”

Instead of eliminating the middle portion of your introduction all together, it might be more prudent to give this information its own section, potentially with subheadings to illustrate the different types of repeats, especially those most conducive to your topic.

Furthermore, in reading through some of your sources, I found the relationship between repeat sequences and disease to be of particular interest. So much of science today deals with translating results from the research lab to clinics. How can we take what we learn at the bench and use it to better understand different diseases and syndromes? Better yet, how can we apply this knowledge to developing treatments and even cures? I believe that a section along these lines would make a great addition to your article. Not only does it further round out what is already shaping up to be a well-structured article, but it also helps to make your topic even more relatable to your audience. With your current sources, you have a great jumping off point for this section. My only caution, in this respect, is that you do not wander off topic, especially given the numerous types of repeats that exist.

In addition, you have handled your sources well. First of all, you have pulled your information from a variety of well-established sources, such as journals. However, I noticed that many of your sources date back to the mid to late 1990s. In keeping with the fact that science is always evolving as we learn more, you may find it helpful to access some information for your remaining sections from more current sources. You may want to try and incorporate some of the newer sources from the reference list in your sandbox. Secondly, it is obvious that you took great care in citing your sources in your text, with some sentences have more than one appropriately placed source. However, I did come across two spots where I would suggest that a citation be added. The first would be at the end of your first paragraph to cover your second and third sentence of that passage. The second would be for the last paragraph of your introduction before you mention the examples.

Upon reading your paper, the first items that drew my attention were your illustration and your examples. In general, these are both excellent ways to not only enhance the content of your text, but also to better reach your audience by providing them with another way to visualize and understand the material. You are already off to a great start in this respect. Being a very visual learn, I can certainly appreciate this approach.

Overall, your article, thus far, is very well thought out and structured based on what I read in your various discussions, and of course, on the article page itself. While you both have expressed an interest in this topic, especially as it relates to your field of study, you have approached your article in a non-biased manner in accordance with Wikipedia guidelines. Furthermore, you have taken care to link key terms and related topics to corresponding Wiki pages, thus allowing you audience to easily navigate and further explore your topic. While this is a science topic, you are obviously striving to make this article as accessible as possible in terms of how the material is presented. Again, this is well assisted by your use of illustrations and examples. I greatly enjoyed reading through your discussions, sources, and article, and I look forward to reading through the final product in December. Good luck!Madscientist2007 (talk) 04:47, 5 November 2013 (UTC)

Hello Madscientist! Thanks for that great review and for getting involved in the topic! Assuming time allows, we will be taking you up on your suggesting to discuss the relation between inverted repeats and disease, so stay tuned for that. Your suggestion on moving the one paragraph makes sense. See our evolving discussion on that topic in the Unit 10 section below. I will personally address the need for the citations you mentioned. As for the rather old dates on the review articles, I see your point but also think it is valid to go back to some of the early articles, particularly those that have been cited a great deal and that provide some of the "foundation" for understanding the basic concepts. For example, plenty of folks still cite the original Watson and Crick article from 1953. None-the-less, we will take your thought on this into consideration as we refine the article. Thanks again for your in-depth review. It is greatly appreciated! -- Jim Perry (Jim892) (talk) 20:17, 11 November 2013 (UTC)

Hello Madscientist, You did a fantastic job going through our article and making very appropriate and insightful comments. Be assured that we have taken to heart each of your comments, and would address them appropriately. Regardless, permit me to comment on a few of your remarks. First, we appreciate your fear that our style seems to show that we may "jump off point". I will address this fear by assuring you that our idea is to define repeats generally, followed by indicating the different repeats, and explaining briefly the differences between inverted repeats and direct repeats. Thereafter, we will address all the issues we have mapped out in our subheadings, albeit in brief, so that we do not present an unnecessarily long article. Again as for your comments on the reference sources, I will agree totally with you that the reference sources we presented so far are a little bit old. The reason for this is that our present write-up, on this topic is introductory. Again, our use of journal articles as our reference sources was deliberate. This is is to enhance the legitimacy of our sources. I would want to point out that most current articles would not dwell on introductions to concepts that are already well known. Their main focus would usually be on the application of these concepts, and I assure you, we will lace our writing with relevant and current citations as we move on to issues that go beyond the present definitions. As I look forward to continuing dialogue with you on this and other articles, I wish to assure you of our commitment to a fine article. Regards. Godwin Ifere 06:16, 12 November 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hi Jim and Godwin,

Thank you for responding back to me. I greatly appreciate the clarifications that you both provided as they helped to give me better insight into your overall plan for this article. You are already off to such a wonderful start with your first contribution. I must say that your illustration and examples are the first things that still draw my eye whenever I go to your article page. These are great additions to the original article, and, as I mentioned in my review, certainly help to make the topic more accessible to your audience (particularly to visual learners like me). I look forward to seeing your additional contribution as your article continues to evolve and to reading the final product come mid-December. I have not doubt that it will be an excellent piece. The best of luck to you both! Madscientist2007 (talk) 03:56, 13 November 2013 (UTC).

Hi Madscientist, Thanks for the keen eye you have on our article. As promised, we have been updating the article as you can see, and I assure you that, each passing day would bring about new additions to the article until we get to our required destination. The bottom portion of the article requires painstaking additions, because of the meaningful explanations expected from us regarding the role of this genetic phenomena in different life situations. Once again, accept our heartfelt thanks for your encouragement and kind words. Kind regards.Godwin Ifere 02:53, 16 November 2013 (UTC)

Your article continues to grow by leaps and bounds. A good portion of the emails in my inbox are notifications of changes to your article, all which have added to what is already a wonderful article. Keep doing what your doing because it is certainly working. Your time and attention to detail is evident as is your consideration of your reviewers comments. I can't wait to see this article when it all finished!Madscientist2007 (talk) 03:31, 23 November 2013 (UTC)

Unit 10 Discussion on article - Molecular Biology Group Project

Hello Godwin. Here are some ideas for our upcoming contributions for Units 10, 12 and 14. Would you be willing to take on the 4 "under construction" sections under "Biological Features and Functionality" during Units 10, 12 and 14? Perhaps spread the work out over those 3 units. I'm planning to write some prose in the Databases section and I've found several more databases to add to the list (and one to remove). Also, I'm thinking about writing a section on "Inverted Repeats and Human Disease" based on a review article I found, but I don't want to infringe on anything you might be covering in those other 4 "under-construction" sections. Let me know if you see a conflict. Also inverted repeats are big with "transposons", so I might write a paragraph/section on that too. Again, let me know if that is ok as I don't want to take away from something you might already have planned. --Jim Perry (Jim892) (talk) 14:07, 11 November 2013 (UTC)

Moving the center portion of the intro as suggested in the above review

Hello Godwin, This topic was brought up by "Madscientist" in the review above. I tend to agree with his comment that it may be too involved for the intro and my suggestion is that we create another sub-section under "Biological Features and Functionality" called "Inverted Repeats and the Human Genome" (perhaps make it the first sub-section) and then simply move the section that Madscientist highlighted. If you agree, I'll be glad to help make the move. It is a little tricky with all those great references included! -- Jim Perry (Jim892) (talk) 20:24, 11 November 2013 (UTC)

Response to comments

Hello Jim, Thanks for going through all the comments and suggestions on how to improve our article. First, I will certainly take on all the subheading and subsections you have mentioned above. I would think we should allow the article to evolve for now, before moving the sections, so that our trend of thoughts would not be distorted. Let me know what you think about this. Regards. Godwin Ifere 06:27, 12 November 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hi Jim, I have started editing the article and would continue daily whenever I find the right articles for citations. You may notice that the publications I am now citing are quite recent. This is because the section I am dealing with now is mostly not on introduction. Take care. Godwin Ifere 07:38, 12 November 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hi Godwin, Holding off on moving the one section is fine with me. Probably good to see what we have in total by about week 15 and then we can adjust/balance if needed. -- Jim Perry (Jim892) (talk) 23:17, 12 November 2013 (UTC)

Hello Godwin, I spent some time adding wikilinks to both the intro section and the database section. You will notice that they now have a lot of "blue" in them. I'm thinking it might be good to do the same thing in the "Biological Features and Functions" section. Let me know if you'd like help with that so we can have the article in top shape by the Friday (Nov 15) extended deadline. If a word matches perfectly with another article, like "exon", then you just put [[ and ]] on either side. If more is needed to match the article name, like the case of wanting "palindromes" to link to the article called "palindromic sequence", the you do this: [[palindromic sequence|palindromes]]. --Jim Perry (Jim892) (talk) 21:51, 14 November 2013 (UTC).

Hi Jim, I have added more to the section Biological Features and functions section, and would continue until we both see that the work is done. I have also seen the beautiful work you have done.I assure you that I will next focus on linking up the articles. Thanks so much for the effort you've put in. Let's keep going on a daily basis. Take Care. Godwin Ifere 02:41, 16 November 2013 (UTC)

Comments from jirwin1097

Hey guys, I am reviewing your article this week. I will be using the rubric to critique in this peer review:

Content coverage

As of right now you guys have four main topics: introduction (lead), understanding repeats/examples, features and functions, and databases.

Introduction is very well done. A definition of “inverted repeats” is provided, the two classes of the repeats are mentioned and briefly explained, and you guys also briefly talk about biological functions. It is concise and very to the point. The only suggestion is to maybe include a sentence or two about how programs databases for repeats exist. According to the Wikipedia guidelines the lead paragraph should be consistent with your outline.

I do have a question/suggestion in the “Biological Features and Functionality” section. In the third subsection “location of inverted repeats in the genome,” the whole paragraph is in quotations. Although this may not be unacceptable, I this subsection would be better if you guys used more of your own words. Again, I don’t think this is in violation of any Wikipedia rule, but I think it can improve the article.

That is all of the advice/suggestions I have for content coverage

Wikilinking

You guys did a great job adding wikilinks to your article. There were only a few that I thought were missing, so I added. I want to make sure you agree, so here is a list of what I added: nucleotides, recombination, conservative site-specific recombination.

References

References are another strong point to your article. Only subsection that one could argue is in need of a reference is the second example. If this is your own example than obviously one isn’t needed. I just wanted to bring this to your attention.

Writing/spelling/grammar/typos

I wasn’t able to find any spelling, grammar, or typographical errors.

Writing organization

Article has a nice flow and all the information is relevant.

Illustrations

I like the two illustrations already added to your article. I think it’s enough, but if you wanted to add another it wouldn’t be a bad idea.

Jirwin1097 (talk) 18:02, 22 November 2013 (UTC)

Hello James! Thanks for the good review. We will definitely apply your suggestions and greatly appreciate the time you spent. We will add something to the intro to mention databases per your suggestion. Thanks for adding the wikilinks that you noticed were missing. We always welcome help from others! And, we can use a reference on that second example so that will be added soon. I like the idea of more illustrations. We will search for those as we do our Unit 12 and Unit 14 contributions. Thanks again for your help! -- Jim Perry (Jim892) (talk) 01:48, 25 November 2013 (UTC)

Unit 11 Comments from Juanquina Thomas

Hello all, I am reviewing your article this week.

The style of your article is very well. As the style guidelines suggests, your introduction is able to stand alone as a concise overview. Being that most people only read the lead paragraph, I think yours is well a great overview of your topic. The wikilinks are good as well. There's one thing I would like to point out in the lead paragraph:

• The style guidelines state that you should not "tease" the reader by hinting at content that follows. The last sentence in your lead paragraph is See "Biological Features and Functionality" section below for more examples -that may be a tease. I'm not sure, just pointing it out. You also have other statements in your lead paragraph that states "see below". Again, I'm not sure if that is the "tease" Wikipedia is referring to, but I wanted to point that out.

The writing is clear and comprehensible.

• There was an interruption of flow because I was unsure if commonest was a word (8th sentence in the introduction). I did some research to find that it is not used often, but it is a word. It is correct, however; I think you may have a few other people like me who stop reading to google the word.

The content of each section fits well. Your examples under "Understanding inverted repeats" are awesome! I think that's that highlight of your article. It is a very thorough example, making the topic easier to understand (hence why the heading "Understanding inverted repeats" fits perfectly!)

I also find your last subsection "Programs and Databases for inverted repeats" to be a nice touch to the article!

Overall, I think you guys have a great article. It is very easy to understand and has a nice flow. I'm looking forward to seeing your final product. Juanquina Thomas (talk) 02:16, 23 November 2013 (UTC)

Hello Juanquina! Thank you for all the great comments and suggestions. I ended up googling "commonest" as well after reading your review. Your suggestion is a good one about not having any "stop words" even if they are technically ok. As for the "tease" in the introduction, I'm going to ask for "higher guidance" on that one from our Online Volunteers. I will refer them to this talk page, so hopefully they will reply. Stay tuned to my section below with this question. Thanks again for your great help! --Jim Perry (Jim892) (talk) 01:54, 25 November 2013 (UTC)

Question about style guidelines

Hello Online Volunteers, Please see the review above by Juanquina Thomas where she brings up the topic of "see below for examples" being a "tease" and thus not in line with the style guidelines for the introduction. We would greatly appreciate your comments on this. Please comment below in this section. Thanks in advance! --Jim Perry (Jim892) (talk) 01:59, 25 November 2013 (UTC)

Yes, I agree with her; it seems like a tease. Instead of that sentence, you might want to, very briefly, summarize or provide another example or two from that section. Klortho (talk) 05:36, 25 November 2013 (UTC)

Ok. Thanks for your help. Just wanted to confirm. I have made the adjustments so we no longer have any "see below" or "see section xyz". And, after making the changes, I like it better! Many thanks to Juanquina for raising this issue! --Jim Perry (Jim892) (talk) 16:53, 25 November 2013 (UTC)

References

Suggest that you run the article through the Citation Bot to populate DOI and PMC fields from your provided PMIDs. (Assumes you're using citation templates) RDBrown (talk) 11:20, 25 November 2013 (UTC)

Hello. Thanks for the suggestion. Could you introduce yourself and tell us about your role with wikipedia? Are you an online volunteer? I checked out your user page but it is basically blank. I'm a student at JHU working on this article with a fellow student and we are on a very tight timeline for this fall semester so may need to prioritize applying this upgrade until after Christmas. Please do not adjust the references in any way until we gain a consensus on changing them as we have invested a lot of time so far. Also could you share the pros/cons of applying this citation bot? I'm confused about why the citation templates don't automatically add the items that you feel are important. Sorry to sound skeptical. Thanks in advance! --Jim Perry (Jim892) (talk) 15:14, 25 November 2013 (UTC)

Ok, I'm an ordinary Wikipedian who mostly adjusts references. If you had been using DIBerri's Wikipedia Template Filling tool (which is now up again at wmflabs now), the url, pmc and doi fields would have been populated if present in the PubMed data. The Citation Bot will populate the doi and pmc fields if it can find the data. It will adjust page ranges to use ndashes and may fix dates. Adding firstn, lastn and editorn fields can be problematic. The advantage of having the doi field is that you can read the full article ... if you have the access, as you will have via JHU. The pmc field gives the link in the PubMed Central collection which is open access. Many journals have now provided DOIs for all of their online articles, the PubMed collection may not have been updated with that data, so running the Citation Bot can still be worthwhile. Running the Bot should take little of your time. Provide the "Inverted repeat" (without quotes) as the article name and your login name and submit. Then use it's history to check what it has done, if necessary edit the article there to remove cluttering parameters.

Please use <ref name=Watson/> for repeated references rather than <ref name=Watson>{{cite book}}</ref>. I'd suggest |first1=James D. |last1=Watson |last2=Tania A. |last1=Baker |last1=Stephen P. |last1=Bell |last1=Alexander |last1=Gann |last1=Michael |last1=Levine |last1=Richard Losik |last1=Stephen C. |last1=Harrison |title=Molecular biology of the gene |publisher=Benjamin-Cummings |location=Boston MA |isbn=9780321762436 |year=2013 |edition=7th |pages= for the cite book parameters itself. It should have the page number range you referenced. If the subsequent references are to other pages add them in as something like Watson, Baker 2013 p. pagenumber. If you ask, I'll fix them to use harvnb templates, but I'd need to check the documentation for that many authors. RDBrown (talk) 22:02, 25 November 2013 (UTC)

Thanks for all the good explanations. Greatly appreciated. We'll try out the citation bot after we wrap up some other priority items. As info... Per your suggestion, I corrected the situations where we accidentally had <ref name=Watson>{{cite book}}</ref> and fixed them up so they now are <ref name=Watson />. Thanks again -- Jim Perry (Jim892) (talk) 14:00, 26 November 2013 (UTC)

Unit 12 Discussion on article - Molecular Biology Group Project

Hello Godwin, I'm working on content for the Unit 12 contributions and thought I'd outline my thinking. I'll take care of getting the "tease" out of the introduction and add something about databases. Perhaps you can respond to the reviewers comments about the one section that is all quotations. As you work on the various sections under "biological features and functions", please let me know if you run into illustrations that would help. We might not be able to simply copy an illustration from a reference, but I'd be glad to take an illustration and draw up something that shows the same concept in a generic way. Let me know if you run into something like that and I'll go to work. Also, I'm planning to add to the "inverted repeats and disease" section for Unit 12 and am still thinking about a section on "transposons", perhaps for Unit 14 if I don't get it done in time for Unit 12. Regards, --Jim Perry (Jim892) (talk) 14:36, 25 November 2013 (UTC)

Hi Jim, This is to notify you that I have commenced work on the article and would continue again tomorrow. I hope to react to all your comments and those of other editors, when next I visit the site. Regards. Godwin Ifere 07:20, 26 November 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hello Jim, I have again added some material to the section on direct versus inverted repeats. You are very free to go through the new addition and make some corrections where necessary. I will keep revisiting the article until it takes the desired shape. Take care. Godwin Ifere 03:48, 3 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Comments from Aconch

Hi all, I’d like to start by complimenting you on your hard work. I took a look at the article history and to see all of the material that has been incorporated since you started working on the article is superb! Overall, I think your article is well written, organized, on-topic, and neutral. Moreover, your sources are reputable and appropriately reflect your article’s content. I particularly like the example section, since it very clearly illustrates the material that you present in the introduction. Below are some minor changes/suggestions that may improve your article:

• Based on prior interactions with the OA, I was notified that the introduction is a general overview for the details that will be cited later in the body. Therefore, unless it is a direct quote, citations are not necessary in this section.

• I hope that you don’t mind, but I restructured a couple of the sentences in your lead section. They now read: “The human genome has many nucleotide sequences that occur repeatedly and as such, can be grouped in two simple classes: repetitive and unique sequences” and “The short tandem repeat sequences are observed in a few to thousands of copies dispersed all over the genome of most eukaryotes.”

• Based on feedback from the OA that I received recently, the headings and the subheadings in an article should follow the structural rules of sentences. Thus, only the first letter of a heading or subheading is capitalized.

• In terms of bolding within the article, I believe that it should only be implemented in the title of the article (along with any synonyms) in the first sentence of the introduction. Other entries in a list should not be bolded. Here is a link for your reference: https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Text_formatting#Boldface

• Your wikilinking was excellent! If you want to add an additional links, I’d suggest wikilinking the following: “transposable elements” (within the Conditions that favor synthesis…headline), and “phage plasmids,” “mitochondria,” and “eukaryotic” (within the Regions where presence is obligatory headline)

• Wonderful illustrations! They were appropriate for the content and easy to see.

• Lastly, I’m not entirely sure if this applies for your Program and databases for inverted repeats section, but Wikipedia mentions that external links “should not normally be used in the body of the article:” https://en.wikipedia.org/wiki/Wikipedia:External_links#What_to_link

Overall, you’ve done fantastic work! Moreover, the suggestions that I mentioned are very minor things and should be relatively easy to fix. I’m certain that your finished product will be a great asset to the Wikipedia community! Aconch (talk) 15:35, 27 November 2013 (UTC)

Hello Aconch. Thanks for the good review. You raise some good points and we will go to work on them. I think we should be ok with the external links on the programs and databases. I've seen other sites with an "External Links" section, but we will do some checking. Thanks so much for your detailed review! --Jim Perry (Jim892) (talk) 23:35, 5 December 2013 (UTC)

Sounds great, Jim. Keep up the good work! Aconch (talk) 18:28, 7 December 2013 (UTC)

Note to Godwin on these items. I have taken care of capitalization and bolding items that Aconch raised in his review. Thanks again to Aconch for pointing these out. --Jim Perry (Jim892) (talk) 19:38, 7 December 2013 (UTC)

Hi guys! You've made some wonderful improvements to the article since my last visit. The formatting makes the article look very polished; I particularly like the colored font for the sequences. It draws your in and it's clear and easy to see. Great job! Aconch (talk) 23:20, 11 December 2013 (UTC)

Unit 14 - Discussion on Article - Molecular Biology Group Project

Hello Godwin. I saw you made some updates to the "direct repeat vs inverted repeat" section. There was typo or something funny with the words "Bold Text" in the second line. (I removed it as I think it was a just a typo.) Also, I think it is confusing to talk about palindromes in this section because "palindromes vs inverted repeats" is the topic of the following section. So, my preference would be to remove the discussion about palindromes from this particular section. Thanks & Regards. --Jim Perry (Jim892) (talk) 17:04, 3 December 2013 (UTC)

Hello again. Looking ahead to Unit 14... I have written a section on "Riboswitches and Inverted Repeats" that I think will fit nicely under the "Biological Features and Functionality" section. I'm going to hold off on posting it until Unit 14 actually starts. I never did anything on "Transposons and Inverted Repeats". Would you be willing to write a section on that topic for Unit 14? Let me know what you think of this idea. It doesn't need to go into too much detail on tranposons, it just needs to describe the role Inverted Repeats play to make them function. There is an image under "Transposable Elements" that might help. I can make a modified version of that image if you want it changed in any way. Also, under "Knockout Rat" (wikipedia article) scroll down to "piggyBac DNA transposon" and there is a good image of inverted terminal repeats that would be an alternative. Regards, --Jim Perry (Jim892) (talk) 17:20, 3 December 2013 (UTC)

Hi. I got an idea from another article to use colors to help distinguish sequences running 5' to 3' or vice versa. I have used blue for 5' to 3' and green for 3' to 5' (same as in the illustration). Then the text to the right side of the illustration (on understanding inverted repeats) had wiki-links that were blue so I removed the wiki-links for just those few sentences. I think this should be ok as the text on the right side of the illustration is basically an additional explanation for the illustration. We have tons of wikilinks elsewhere in the article. --Jim Perry (Jim892) (talk) 01:33, 5 December 2013 (UTC)

Hello Jim, I am looking at your proposal fro a write up on Riboswithches and Inverted repeats for Unit 14. I should come up with something over the weekend. Thanks for keeping our article improved. Godwin Ifere 03:32, 5 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hi Godwin... PLEASE NOTE.... I have already written something on Riboswitches, just haven't posted it yet. Please do a section on Transposons and Inverted Repeats instead! Thanks. --Jim Perry (Jim892) (talk) 23:19, 5 December 2013 (UTC)

Comments from Agulati4

The current article is a vast improvement over the original article! Overall, everything looks great. All of the sections add to the article and help provide a complete overview of what an inverted repeat is, where it is located, and how it can be seen in diseases. The article is very well organized, neutral, and clear and concise. The images also add to the understanding of each section. In particular, I really like how you have added a section on programs and databases used to locate inverted repeats. I just have a few minor suggestions. First, make sure to appropriately wiki link scientific words. For instance, “repeated sequences” in the lead section/introduction is linked twice. Second, make sure to properly cite (i.e. in line citations generally go after the period). Third, some sentences should be rephrased. For instance, under the “Conditions that favor inverted repeats” category, where it states “Very stable chromosomes have been observed with a comparatively fewer number of inverted repeats than direct repeats, suggesting a relationship between the stability of and the number of repeats.” Since the sentence is discussing chromosome stability, you could rephrase the sentence as follows: Very stable chromosomes have been observed with comparatively fewer numbers of inverted repeats than direct repeats, suggesting a relationship between chromosome stability and the number of repeats. Also, under the "Programs and Databases for Inverted Repeats," the sentence describing Inverted Repeats Database has two cans in it. In addition, you could also add information about the inverted repeat involved in transcription termination. Overall, great job! The article is looking great and I am very excited to see the final version! Please let me know if you have any questions on any of the suggestions! - Agulati4 (talk) 18:30, 5 December 2013 (UTC)

Thanks Agulati4 for your good review. I have fixed up the double "can can" and also the repeated wikilinks of the same item. Good catches! You must be a professional proofreader! We fixed up a bunch of the references, but will take another look. I'll pass the sentence rephrase on to my partner for his consideration. Thanks much for your help. --Jim Perry (Jim892) (talk) 23:28, 5 December 2013 (UTC)

Hi Jim! Thank you for your response! I'm glad my suggestions helped. The article is looking great and I am definitely looking forward to seeing the final version! Good luck! - Agulati4 (talk) 00:53, 13 December 2013 (UTC)

Comments from Galemu2

Hello Jim. You have done a great job on improving this article. It’s a well-organized and clearly written article. The lead section clearly establishes context and boundaries for the articles. The context of the article seem relevant to the topic. I have few suggestions that may improve the article.

• It is not necessary to add citation in the lead section unless it’s a direct quotes.
• I suggest adding add a sidebar liking to related topics such as microsattellites, minisatellites, tander arrays, centromere and telomere. I might have missed something.
• The content of the first section seems necessary for understanding the rest of the article. However, it may sound better if you just call it “Examples of an inverted repeats” insade of “Understanding Inverted Repeats”.
• The subsection “conditions that favor synthesis of inverted repeats” uses the same inline citation multiple times. This may be replaced with a single inline citation at the end to reduce citation density.
• In the section “Inverted Repeats, Mutations, and Disease” the text specifies where the image is located. Generally the text should not specify where the image is located.
• My suggestion is placing the text that describes the image inside the caption and not as a paragraph of the section.
• I recommend putting this image in the lead section, because it exemplifies the alternate conformation of inverted repeats
• The “Genetics:repeted seqence” navigation box should be placed below the “see also” section and above the references.

In general it was very informative reading the article. The contexts of the article are very relative to the article. I actually enjoyed the “programs and databases” section. Keep up the good work. Galemu2 (talk) 19:53, 7 December 2013 (UTC)

Hello Galemu2. Thanks for your review of our article. I fixed up many of the items you mentioned above and I thank you for the suggestions. The text specifying image location is now gone and we will go to work on the others. We have received many favorable comments about the phrase "Understand inverted repeats" for the first section, so we will probably stay with that but we do appreciate your suggestion. The sidebar is a great idea and we'll definitely look into that. Thanks again for your good input! --Jim Perry (Jim892) (talk) 21:54, 7 December 2013 (UTC)

Hi Galemu2. Thanks you very much for the great attention you've paid to our article. Your comments are also very helpful, and I am in touch with Jim about what to do with some of the issues you have raised. For the inline citations, I have had comments that they were well made. The essence of duplication in some case as you well know is to avoid plagiarism. Nonetheless, expect us to review the article in the next few days. Accept our regards. Godwin Ifere 03:35, 12 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hello Wenwatata. Hope all is well. I can see that you have added a sidebar in the lead section. Sidebars make it easier to learn about the topic. Also, hope you don't mined that i edited the size in the "Inverted repeats in riboswitches" subsection. The image was bigger than the page size. I also wanted to change the size of the inverted repeat example image, but i don't know how attached you are to the image. It might help to reduce the size of the image, for the look of the article. Keep up the good work.Galemu2 (talk) 04:49, 14 December 2013 (UTC)

Hello Galemu2. Please leave the images sized the way we have them. I've spent a lot of time trying to get the optimum look. When the images are reduced in size, they lose clarity. The riboswitch image was set to 850 px and you mentioned that it was bigger than the page size. What "page size" are you referring to? It looked great on my laptop and on my desktop. Most computers these days are at least 1024 wide if not more. Thanks in advance for clarifying. Regards. --Jim Perry (Jim892) (talk) 05:10, 14 December 2013 (UTC)

Hello again and here is an update on the file size issue. I took another look and now see that the left border of Wikipedia is taking up about 250 px and so 850 px is just a bit too large for a 1024 px screen width. I modified the illustration by pushing the items closer together and we can now get good clarity with 800 px as the width (which is 50% of the actual illustration width). I set my browser width to 1024 px and it worked ok. Please let me know how it looks on your computer. Thanks much. --Jim Perry (Jim892) (talk) 06:12, 14 December 2013 (UTC)

Hi Jim892. I have to apologize. I forgot i had my browser zoomed in. The default text size is kind of small to see. That made the image seem bigger than the browser window. Your size actually works for a normal screen. Galemu2 (talk) 17:38, 14 December 2013 (UTC)

Comments from Klortho

• This bit from the lead could use some rewording: "... that occur repetitively. The human genome has many nucleotide sequences that occur repeatedly and as such, can be grouped in two simple classes: repetitive and unique sequences." I find it very confusing, because I thought the "two simple classes" were two classes of repeats. I think that last clause could be dropped.
• "commonest" → "most common"
• I think you need to make a distinction between inverted and direct repeats in the lead, because that is where you talk about things like tandem arrays, etc. Some of the things you mention are not inverted repeats, and I think this is a crucial detail, and should be made very clear.
• Don't link from the lead to later sections within the same article ("programs and databases").

• Nice figure!! I'm really impressed. It is always hard to explain the concept of inverted repeats, and this illustration really does a good job. Nice work!
• This sentence does not scan: "There is similarity between direct and inverted repeat, or else a palindrome, with the exception of the second half of the inverted repeat positioned in the complementary strand as follows". I don't understand what you are trying to say.
• "Location of inverted repeats in the genome" - why is this whole section in quotes?
• "Inverted repeats, mutations, and disease"
  • I think "acclaimed" is the wrong word choice.
• I haven't read the whole article, but most of what I have read is written at too technical a level. Keilana suggests that you write for a smart 15-year old high school student. I think, whatever you could do between now and the end of the semester to make the article more accessible, would improve it greatly.

Good job! Klortho (talk) 02:14, 9 December 2013 (UTC)

Hello Klortho. Thanks for all the good comments. We will go to work on these right away. Regards. --Jim Perry (Jim892) (talk) 10:55, 9 December 2013 (UTC)

Hi Klortho. I have noted your keen eye on the articel and I would set to work as soon as Jim and I agree on what to to do. Be assured we'll seriously consider your suggestions. Thanks. Godwin Ifere 03:24, 12 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

The link in the intro on "programs and databases" that took a reader to that section within this article has now been removed per the above suggestion. Thanks! --Jim Perry (Jim892) (talk) 21:52, 12 December 2013 (UTC)

Progress report

• Expanded subsection on direct repeat versus inverted repeat
• Use illustrations in color to emphasize the different types of repeat
• Added material to subtitle on Biological features and functionality
• Removed some subheadings that seem redundant
• Expanded section on inverted repeat, mutations and disease
• Added figures on the preceding section for illustrative purposes Godwin Ifere 04:26, 12 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Unit 14 - Discussion (part 2) on Article

Hello Godwin. The semester is almost over! The earlier discussion on Unit 14 was so large I decided to start this "part 2". I took a shot and simplifying the "direct repeat" section a bit as we had several reviewers making comments on it. I kept the old version of this section in the article and just "commented it out" so we can easily restore it if needed. Here is what I did, let me know if you it is ok with you. First, I adjusted the example to match the example immediately above so the reader doesn't have multiple sequences to understand. Second, I removed the sentences pertaining to palindromes because that topic is addressed in the next section. The section is smaller now, but I think that is ok because it is just there as a comparison point with inverted repeats.

Couple of other items... I added a "sidebar" per one of the reviewer's suggestion. It is to the right of the "contents" box. It is a collection links to the related topics in alphabetical order. Feel free to add to the list. Just duplicate one of the existing lines in the code and insert the new item on its own line (in the correct alpha order of course). I also added a section on Riboswitches with a graphic that I drew. Please let me know if you need any help with any graphics.

Also, the "progress report" that you wrote looks good, but it is supposed to be posted on the "Group 84D" page. I made a copy of it there and will add some additional items. Thanks for writing it! Here is the link to the Group 84D page. It is now in place, so it would be best if you deleted the old copy from this talk page.

Thanks and regards! --Jim Perry (Jim892) (talk) 00:22, 13 December 2013 (UTC)

Hello Jim, Thanks you for the work you continue doing on our article. This shows that you'll continue visiting the site way beyond the semester. I will do the same too. Let me commend you for the addition to the article. It has taken a new look that makes it far better than when we started. I have read through the addition. I extended the first sentence in subsection on riboswitches. Since wiki for the general audience, I felt it was necessary to define certain terminologies like riboswitches, which may seem esoteric. I totally agree with your cation on the reviewers comments. You only went a bit faster, as I was about doing the same. Finally, the graphic on riboswitches was catchy to the eye. I hope to maintain contact with you. You are indeed a great guy and partner to work with. Accept my warmest regards. Godwin Ifere 04:25, 15 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hi Jim, once again, thanks for repositioning the progress report, and making additions to what I did earlier. Accept my thanks again. Godwin Ifere 04:27, 15 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Comments from Juanquina Thomas

Hello all. I was stopping by to do a final read on your article. Your progress with this article is great, and I really felt like your content was very easy to read. I think the visuals for this article were a plus as well. Good luck to you guys! Juanquina Thomas (talk) 02:58, 15 December 2013 (UTC)

Hi Juanquina, We really appreciate the time taken to reviewing our article. We also thank you for your support, encouragement and appreciation of our work.Godwin Ifere 03:58, 15 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Misc cleanups

I did a quick pass to fix some layout details according to the Manual of Style. One MOS item I did not do was to remove some of the caption-text (simple image-title, source-credit) from the images themselves, per Wikipedia:Manual of Style/Captions. DMacks (talk) 03:48, 15 December 2013 (UTC)

For example, WP:BIDIRECTIONAL says we should not have a loose list of "see also" types of articles at the top-right in general (especially not as a simple list if they are of different levels of detail or association). And MOS:IMAGELOCATION explicitly instructs to have the first image on the right, and to include them within the section where they are relevant instead of dangling down from the previous. Likewise, you'll want to avoid using such large images in some cases (where there is not a lot of detai) because the page is overwhelmed by some of them and annoying to read on small screens because of it. Especially File:Antithrombin-gene-strand-switch.gif and the other one like it...the in-image base letters are 2–3x the size of the article prose itself and the image really is only secondary to the prose (at most, the key parts that are already highlighted by color and box really "matter"). The MOS really is important to follow because many people spent years experimenting and finding what works best overall especially for diverse readers rather than what the primary author(s) think looks best. DMacks (talk) 04:04, 15 December 2013 (UTC)

Hi DMacks. As you can see from the talk page notes above, this is a Course Project and our deadline is this weekend. If at all possible, please post your suggestions in this talk page so that we can learn from you and so that you afford us the courtesy of not simply "blowing away" items that we have spent time developing. Please keep in mind the Fourth and Fifth Pillars of Wikipedia... "Editors should be respectful of each other" and "Wikipedia has no firm rules". I performed and "undo" on two of your five changes for the following reasons... The placement and size of the first illustration was discussed by many and that placement and size is a result of a consensus view of editors working on this project and reviewers of the project. Likewise the sidebar was also the result of a reviewer's suggestion. Please don't impose your view of how the article should look without first discussing with us and reaching a consensus. Thanks and Regards, --Jim Perry (Jim892) (talk) 04:23, 15 December 2013 (UTC)

I'm sympathetic to student projects (and the impending end of the US academic semester).As collaborative editors, we all need to also consider the wider WP guidelines rather that "just" what is said here on the talkpage specific to an article. It's easy to lose sight of the broader perspective of WP as an encyclopedia for all rather than just a medium for your own course (plus risk of an echo chamber among a small group in general). For example, why is it better to have an image "part of" a section other than the prose that actually discusses it?--please point me to that item in the above discussions, as I cannot find it. That's an explicit guideline, and I assume you want to demonstrate that you are following sitewide guidelines for your class or (as usual per "WP guideline" guidelines, have an explicit reason for not doing so. Be careful: WP:IAR is well known to mean solely "...for the betterment of the encyclopedia", not anything like "a do whatever I want because I want to" anarchy. The sidebar might be a useful idea, but it's not done according to the guideline for sidebars (that guideline was explicitly mentioned when the idea was proposed above). DMacks (talk) 04:35, 15 December 2013 (UTC)

Confusing image

File:DNA palindrome.svg is a little confusing because it uses different letters to refer to the same base-sequences. If the goal is to illustrate how the same chain changes pairing, it should use the same label to identify each region to make it easier to see which piece has gone. That would improve ease of understanding in general, and avoid relying on color or reading the small letters of the specific bases to track the key relationships (see WP:ACCESSIBILITY). For example, call the two regions in the straight chain "A1" and "A2" and their complementary regions "A1'" and "A2'". Then in the stem-loop form, label "A1" and its now-complement "A2", and likewise "A1'" and "A2'". You could draw a box around the "stem" and "loop" regions and label them as such. DMacks (talk) 04:20, 15 December 2013 (UTC)

Thinking further, something like that would make a good lede image (something WP guidelines say should exist, and was even mentioned in a previous comment up-page). No need to include any base labels, maybe just a Ribbon diagram-like arrow indicating 5'→3' in boxed regions labeled "A" and "A'". DMacks (talk) 05:15, 15 December 2013 (UTC)

Final comments from Juanquina Thomas

Hi guys. I was just stopping by to give my final comments on your article. I would just like to say that your article was my favorite. It was very descriptive and plainly written for those who may not understand the sciences. I enjoyed all of your examples, explanations, etc. I think you guys did a great job. Congrats! Juanquina Thomas (talk) 04:59, 15 December 2013 (UTC)

Merge discussion

@Petr Matas: opened a merge template on October 14, 2020. I am not sure what to think about the proposal yet, but we need to have a discussion section.--Artoria2e5 🌉 09:56, 17 December 2020 (UTC)

@Artoria2e5: According to article Inverted repeat, we have:

• Inverted repeat with zero intervening length = palindromic sequence
• Inverted repeat with non-zero invervening length

I think that most statements and uses apply to both, but they are split into two articles. Petr Matas 06:58, 20 December 2020 (UTC)

I am not too well-versed on this topic, but I mean the Vs. palindrome part already looks like the correct description, albeit there is apparently enough to talk about palindromes on their own. I am not against merging nor keeping them separate - if kept separate, maybe it'd be better to just use {{Main}} to inform the reader where to get more information. KingisNitro (talk) 12:54, 21 July 2021 (UTC)

Closing, with no merge, given what seems to be a preference to distinguish and added linking templates, rather than to merge. Klbrain (talk) 12:21, 21 October 2021 (UTC)

Resolved