Answers.Body: <p>(<em>Should be a comment not an answer, but I weary of SE comment formatting- feel free to express disapproval in whichever way</em>)</p>
  <p>When in doubt, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029072/" rel="nofollow noreferrer">google it</a> and look at <a href="https://en.wikipedia.org/wiki/Trie" rel="nofollow noreferrer">wikipedia</a>:</p>
  <blockquote>
  <p>Tries are used in Bioinformatics, notably in sequence alignment software applications such as BLAST, which indexes all the different substring of length k (called k-mers) of a text by storing the positions of their occurrences in a compressed trie sequence databases.[25]</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-06T18:30:09.627Z
Answers.LastActivityDate: 2023-12-06T18:30:09.627Z
Answers.UserDisplayName: Maximilian Press
Body: <p><em>This question was also asked on <a href="https://www.reddit.com/r/bioinformatics/comments/18epsi0/what_are_some_bioinformatics_applications_for/" rel="nofollow noreferrer">reddit</a></em></p>
  <p>Tries are a data structure that can be used to efficiently store and search for strings.
  Tries created from an <em>ordered sequence of strings</em>  differ from the regular Tries in the following way:</p>
  <p>If there is a string of a certain character <span class="math-container">$w$</span> at a character position <span class="math-container">$x$</span> and is between two other strings that have both the same character <span class="math-container">$p$</span> where <span class="math-container">$p \neq
   w$</span> at position <span class="math-container">$x$</span>(and all their characters before position <span class="math-container">$x$</span> are the same in all three strings) then the Trie must have an edge for the first occurrence of <span class="math-container">$p$</span>, an edge for <span class="math-container">$w$</span> and an edge for the second occurrence of <span class="math-container">$p$</span>.</p>
  <p>I have recently written a paper regarding a novel data structure that is related to tries and I wish to connect it to some applications in bioinformatics since the paper itself presents only one application related to string algorithms.</p>
  <p>Since bioinformatics makes some use of string algorithms and since the structure is related to Tries I wish to ask you about the possible applications of Tries so I may find some application to my related data structure.</p>
  <p>What are the applications of Tries(data structure) of an <em>ordered
  sequence of strings</em> in bioinformatics?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-12-01T11:01:12.420Z
Comments.Text: This seems a bit like an answer searching for a question. Discussion-based questions don't work so well here, and are better asked on discussion sites like [reddit](https://Reddit.com/r/bioinformatics). Are you able to clarify your particular problem and relate it to a specific bioinformatics problem?
Comments.UserDisplayName: gringer
Tags: <phylogenetics><genomics><algorithms>
Title: What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
ThreadText: # What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
  
  (Asked by: username_0 on 2023-11-28)
  
  *This question was also asked on [reddit](https://www.reddit.com/r/bioinformatics/comments/18epsi0/what_are_some_bioinformatics_applications_for/)*
  
  Tries are a data structure that can be used to efficiently store and search for strings.
  Tries created from an *ordered sequence of strings* differ from the regular Tries in the following way:
  
  If there is a string of a certain character $w$ at a character position $x$ and is between two other strings that have both the same character $p$ where $p \neq
  w$ at position $x$(and all their characters before position $x$ are the same in all three strings) then the Trie must have an edge for the first occurrence of $p$, an edge for $w$ and an edge for the second occurrence of $p$.
  
  I have recently written a paper regarding a novel data structure that is related to tries and I wish to connect it to some applications in bioinformatics since the paper itself presents only one application related to string algorithms.
  
  Since bioinformatics makes some use of string algorithms and since the structure is related to Tries I wish to ask you about the possible applications of Tries so I may find some application to my related data structure.
  
  What are the applications of Tries(data structure) of an *ordered
  sequence of strings* in bioinformatics?
  
  **Tags:** phylogenetics, genomics, algorithms
  
  > **Comments:**
  > **username_1**: This seems a bit like an answer searching for a question. Discussion-based questions don't work so well here, and are better asked on discussion sites like [reddit](https://Reddit.com/r/bioinformatics). Are you able to clarify your particular problem and relate it to a specific bioinformatics problem?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-12-06. Score: 1
  
  (*Should be a comment not an answer, but I weary of SE comment formatting- feel free to express disapproval in whichever way*)
  
  When in doubt, [google it](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029072/) and look at [wikipedia](https://en.wikipedia.org/wiki/Trie):
  
  > Tries are used in Bioinformatics, notably in sequence alignment software applications such as BLAST, which indexes all the different substring of length k (called k-mers) of a text by storing the positions of their occurrences in a compressed trie sequence databases.[25]
  
  
  ---
  
  