Answers.Body: <ul>
  <li>GGGG,gggg,GGGG,GGGG,UUUU</li>
  </ul>
  <p>Quadbase appears to be about DNA secondary structures, albeit the above example is RNA. The website states,</p>
  <blockquote>
  <p>G-Quadruplexes or G4s are secondary DNA structures that are now established to have functionally crucial roles in various cellular processes.</p>
  </blockquote>
  <p>Two guesses, firstly its all just a bit weird, secondly its a representation of hypoxanthine. Its more likely to be the second guess than the first.</p>
  <ol>
  <li>The nomenclature is a bit weird: gggg with UUUU would infer non-canonical binding/bounding in <a href="https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html" rel="nofollow noreferrer">WUSS</a> (Washington University Secondary Structure) format for a psuedoknot  (type of secondary structure). If that wasn't the interpretation it would be kinda weird to share nomenclature with a major secondary structure format (WUSS) for secondary structure notation.</li>
  </ol>
  <p>The 'dots', i.e. '.' appear to represent continuation, although in dot-bracket format (secondary structure format) this represents a nucleotide that doesn't hybridise.</p>
  <hr />
  <ol start="2">
  <li>Its worth reading the paper for hypoxanthine representation (normally its 'I'), because 'I' will behave like a guanine residue and would then make sense if it was being represented as 'g'. Thus, the following means no hypoxanthine,</li>
  </ol>
  <ul>
  <li>GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…</li>
  </ul>
  <p>My bet is its point 2, otherwise it doesn't make sense.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-25T02:21:12.633Z
Answers.LastActivityDate: 2022-08-25T13:01:34.710Z
Answers.LastEditDate: 2022-08-25T13:01:34.710Z
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Body: <p>What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below:</p>
  <ul>
  <li>GGgG,GGgG,GGgG,GGgG,GGGG,GGGG…</li>
  <li>GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…</li>
  <li>GGGG,gggg,GGGG,GGGG,UUUU</li>
  <li>ggGg,ggGg,ggGg,GGgG,GGgG,GGgG…</li>
  </ul>
  <p>These sequences are real experimental samples. I obtained them from QuadBase. Here is the link below:</p>
  <p><a href="https://quadbase.igib.res.in/" rel="nofollow noreferrer">https://quadbase.igib.res.in/</a></p>
  <p>Hopefully you will provide some literature within the thread in order to understand this concept in bioinformatics.
  BTW I'm a beginner in this field and hopefully this
  Bioinformatics Stack Exchange site will help me find out the answers.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-25T12:24:30.873Z
Comments.Text: Please [edit] your question and tell us exactly how you got these sequences. You have linked to a page with various tools, which one gave you this output? What was your input? The meaning of upper vs lower case can vary enormously depending on context. for example, in genomic sequences, lowercase letters often mean low complexity regions, but we need to know more about these specific sequences and how you got them to be able to help you. Have you looked at the quadbase paper? http://nar.oxfordjournals.org/content/early/2016/05/16/nar.gkw425.full
Comments.UserDisplayName: terdon
Tags: <phylogenetics><genome><ngs><database>
Title: Lower case vs. upper case nucleotids in sequence vs. dots at the end
ThreadText: # Lower case vs. upper case nucleotids in sequence vs. dots at the end
  
  (Asked by: username_0 on 2022-08-25)
  
  What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below:
  
  * GGgG,GGgG,GGgG,GGgG,GGGG,GGGG…
  * GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…
  * GGGG,gggg,GGGG,GGGG,UUUU
  * ggGg,ggGg,ggGg,GGgG,GGgG,GGgG…
  
  These sequences are real experimental samples. I obtained them from QuadBase. Here is the link below:
  
  <https://quadbase.igib.res.in/>
  
  Hopefully you will provide some literature within the thread in order to understand this concept in bioinformatics.
  BTW I'm a beginner in this field and hopefully this
  Bioinformatics Stack Exchange site will help me find out the answers.
  
  **Tags:** phylogenetics, genome, ngs, database
  
  > **Comments:**
  > **username_1**: Please [edit] your question and tell us exactly how you got these sequences. You have linked to a page with various tools, which one gave you this output? What was your input? The meaning of upper vs lower case can vary enormously depending on context. for example, in genomic sequences, lowercase letters often mean low complexity regions, but we need to know more about these specific sequences and how you got them to be able to help you. Have you looked at the quadbase paper? http://nar.oxfordjournals.org/content/early/2016/05/16/nar.gkw425.full  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-08-25. Score: 0
  
  * GGGG,gggg,GGGG,GGGG,UUUU
  
  Quadbase appears to be about DNA secondary structures, albeit the above example is RNA. The website states,
  
  > G-Quadruplexes or G4s are secondary DNA structures that are now established to have functionally crucial roles in various cellular processes.
  
  Two guesses, firstly its all just a bit weird, secondly its a representation of hypoxanthine. Its more likely to be the second guess than the first.
  
  1. The nomenclature is a bit weird: gggg with UUUU would infer non-canonical binding/bounding in [WUSS](https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html) (Washington University Secondary Structure) format for a psuedoknot (type of secondary structure). If that wasn't the interpretation it would be kinda weird to share nomenclature with a major secondary structure format (WUSS) for secondary structure notation.
  
  The 'dots', i.e. '.' appear to represent continuation, although in dot-bracket format (secondary structure format) this represents a nucleotide that doesn't hybridise.
  
  ---
  
  2. Its worth reading the paper for hypoxanthine representation (normally its 'I'), because 'I' will behave like a guanine residue and would then make sense if it was being represented as 'g'. Thus, the following means no hypoxanthine,
  
  * GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…
  
  My bet is its point 2, otherwise it doesn't make sense.
  
  
  ---
  
  