Answers.Body: <p>A brief literature review can give you the answers.</p>
  
  <p><a href="https://arxiv.org/abs/1305.4883" rel="nofollow noreferrer">This preprint</a> gives the definition of RFLCS more clearly:</p>
  
  <blockquote>
    <p>A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once.</p>
  </blockquote>
  
  <p><a href="https://www.sciencedirect.com/science/article/pii/S0166218X09001802" rel="nofollow noreferrer">Adi et al</a> proposed to solve the <a href="https://en.wikipedia.org/wiki/Chromosomal_rearrangement" rel="nofollow noreferrer">genome rearrangement</a> problem raised in <a href="https://www.ncbi.nlm.nih.gov/pubmed/10743557" rel="nofollow noreferrer">this paper</a>. If you want to know more, follow the references and citations of these papers and read them.</p>
  
  <p>Basically, Adi et al think the length of RFLCS measures the distance between two genomes. The longer the more similar. I am not sure if this is a good measurement, though.</p>
  
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Answers.CreationDate: 2019-03-03T19:00:10.457Z
Answers.Text: Now I see. If shifts in LCS were solely the consequence of rearrangements .. yes, but we all know thats not true. Transposons move, microsatellites, minisatellites and DNA virus integration (e.g. HPV) will all be confounders,
Answers.UserDisplayName: M__
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Answers.CreationDate: 2019-03-09T12:41:44.650Z
Answers.Text: Thanks for the answer. I read several papers, but no one explains why RFLCS should be a good measure. Seems nobody have assessed its effectivness.
Answers.UserDisplayName: Daniele Cuomo
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Answers.CreationDate: 2019-03-09T14:21:56.013Z
Answers.Text: @DanieleCuomo I don't think RFLCS will be effective, tbh.
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Answers.UserDisplayName: user172818
Body: <p>I'm starting a thesis in Computer Science with topic the RFLCS (Repetition-free Longest Common Subsequence). I know very little about Bioinformatics problems and Genomics. I would like to understand the motivations behind this problem.
  More precisely, I'd like to understand why one need a similarity measure between genomes, and how the RFLCS is an useful measure.</p>
  
  <p>[Adi et al.] introduce the problem in <a href="https://www.sciencedirect.com/science/article/pii/S0166218X09001802" rel="nofollow noreferrer">this article</a>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-02T18:57:39.833Z
Comments.Text: What is the RFLCS? PLease [edit] your question and give us some more detail so we can understand exactly what you're asking. However, I am afraid that this will probably be too broad to answer (see the "too broad" section here: https://bioinformatics.stackexchange.com/help/closed-questions).
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2019-03-02T19:04:40.000Z
Comments.Text: Done! I narrowed the field, hope enough.
Comments.UserDisplayName: Daniele Cuomo
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Comments.CreationDate: 2019-03-02T20:49:03.020Z
Comments.Text: Still a bit obscure. I think the question is there to sharpen your coding skills. Its fairly easy to solve. Although it could be solved as a 5% tail of a Poisson distribution (I doubt that is what its about).
Comments.UserDisplayName: M__
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Comments.CreationDate: 2019-03-03T19:38:05.923Z
Comments.Text: I found [the paper introducing it](https://www.sciencedirect.com/science/article/pii/S0166218X09001802) and I think you should mention it in the question. I think that your supervisor is the best person to talk to regarding motivations of the problem. If there is anything you would like to get help with from the community, you need to be more concrete. "Why do I do my thesis" is way too broad.
Comments.UserDisplayName: Kamil S Jaron
Tags: <genomics>
Title: Repetition-free Longest Common Subsequence as similarity measure
ThreadText: # Repetition-free Longest Common Subsequence as similarity measure
  
  (Asked by: username_0 on 2019-03-02)
  
  I'm starting a thesis in Computer Science with topic the RFLCS (Repetition-free Longest Common Subsequence). I know very little about Bioinformatics problems and Genomics. I would like to understand the motivations behind this problem.
  More precisely, I'd like to understand why one need a similarity measure between genomes, and how the RFLCS is an useful measure.
  
  [Adi et al.] introduce the problem in [this article](https://www.sciencedirect.com/science/article/pii/S0166218X09001802).
  
  **Tags:** genomics
  
  > **Comments:**
  > **username_1**: What is the RFLCS? PLease [edit] your question and give us some more detail so we can understand exactly what you're asking. However, I am afraid that this will probably be too broad to answer (see the "too broad" section here: https://bioinformatics.stackexchange.com/help/closed-questions).  
  > **username_0**: Done! I narrowed the field, hope enough.  
  > **username_2**: Still a bit obscure. I think the question is there to sharpen your coding skills. Its fairly easy to solve. Although it could be solved as a 5% tail of a Poisson distribution (I doubt that is what its about).  
  > **username_3**: I found [the paper introducing it](https://www.sciencedirect.com/science/article/pii/S0166218X09001802) and I think you should mention it in the question. I think that your supervisor is the best person to talk to regarding motivations of the problem. If there is anything you would like to get help with from the community, you need to be more concrete. "Why do I do my thesis" is way too broad.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2019-03-03. Score: 1
  
  A brief literature review can give you the answers.
  
  [This preprint](https://arxiv.org/abs/1305.4883) gives the definition of RFLCS more clearly:
  
  > A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once.
  
  [Adi et al](https://www.sciencedirect.com/science/article/pii/S0166218X09001802) proposed to solve the [genome rearrangement](https://en.wikipedia.org/wiki/Chromosomal_rearrangement) problem raised in [this paper](https://www.ncbi.nlm.nih.gov/pubmed/10743557). If you want to know more, follow the references and citations of these papers and read them.
  
  Basically, Adi et al think the length of RFLCS measures the distance between two genomes. The longer the more similar. I am not sure if this is a good measurement, though.
  
  > **Comments:**
  > **username_2**: Now I see. If shifts in LCS were solely the consequence of rearrangements .. yes, but we all know thats not true. Transposons move, microsatellites, minisatellites and DNA virus integration (e.g. HPV) will all be confounders,  
  > **username_0**: Thanks for the answer. I read several papers, but no one explains why RFLCS should be a good measure. Seems nobody have assessed its effectivness.  
  > **username_4**: @username_0 I don't think RFLCS will be effective, tbh.  
  
  ---
  
  