Answers.Body: <p>You are correct, it is the score of the candidate protein against the BUSCO profile hmm assessed by hmmer. If it passes a threshold, it is validated as being that BUSCO gene. The threshold is defined for each profile based on the score of the species used to produce the profile. It can be found in <code>name_odb10/scores_cutoff</code>. And yes, the higher the better.</p>
  
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Answers.CreationDate: 2020-03-16T14:52:28.960Z
Answers.Text: Welcome, Mathieu! And thanks for the answer.
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2020-03-16T13:44:46.417Z
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Answers.UserDisplayName: Mathieu
Body: <p>The BUSCO <code>_full_table.tsv</code> output has scores per gene (an example bellow).</p>
  
  <p>In <a href="https://academic.oup.com/bioinformatics/article/31/19/3210/211866" rel="nofollow noreferrer">the original publication</a>, authors just mention a condition to satisfy a bitscore, but I could not find what the bitscore actually is. In the <a href="https://busco.ezlab.org/busco_userguide.html" rel="nofollow noreferrer">use guide</a> they say</p>
  
  <blockquote>
    <p>If found to be complete, whether single-copy or duplicated, the BUSCO
    matches have scored within the expected range of scores ...</p>
  </blockquote>
  
  <p>but again, I don't understand what the score actually represents. I am even not sure if greater the better or visa reverse. Does anybody know what the score is?</p>
  
  <pre><code># BUSCO version is: 4.0.2 
  # The lineage dataset is: insecta_odb10 (Creation date: 2019-11-20, number of species: 75, number of BUSCOs: 1367)
  # Busco id      Status  Sequence        Gene Start      Gene End        Score   Length
  47at50557       Complete        scf1:20448-42284    20448   42284   4607.1  3554    https://www.orthodb.org/v10?query=47at50557     Immunoglobulin-like domain
  547at50557      Complete        scf2:9780-23590    9780    23590   2743.8  1555    https://www.orthodb.org/v10?query=547at50557    protein unc-80 homolog
  755at50557      Complete        scf3:9036-28083    9036    28083   3149.9  2206    https://www.orthodb.org/v10?query=755at50557    SRCR-like domain
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-15T20:06:22.400Z
Comments.Text: Interesting question, its not immediately obvious I definitely agree
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T09:19:06.633Z
Comments.Text: I don't think any of the guys from the Zdobnov lab are on this site yet, but do raise an issue on gitlab https://gitlab.com/ezlab/busco
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T09:20:07.630Z
Comments.Text: i recall that the bitscore cutoffs are HMMER3 thresholds that are tailored for each individual profile (i.e. model-specific), but since i never worked on BUSCO i might be wrong
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T09:38:20.023Z
Comments.Text: Thanks folks. If you are right about HMMER, then it is "A HMMER bit score is the log of the ratio of the sequence’s probability according to the profile (the homologyhypothesis) over the null model probability (the non-homology hypothesis)."
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T09:39:41.230Z
Comments.Text: I might as well invite Mathieu Seppey, I think it would be healthy to have him around :-).
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T14:53:15.023Z
Comments.Text: @Chris_Rands There you go, we got now! ^^
Comments.UserDisplayName: Kamil S Jaron
Tags: <busco>
Title: What is the per-gene score in BUSCO output?
ThreadText: # What is the per-gene score in BUSCO output?
  
  (Asked by: username_0 on 2020-03-15)
  
  The BUSCO `_full_table.tsv` output has scores per gene (an example bellow).
  
  In [the original publication](https://academic.oup.com/bioinformatics/article/31/19/3210/211866), authors just mention a condition to satisfy a bitscore, but I could not find what the bitscore actually is. In the [use guide](https://busco.ezlab.org/busco_userguide.html) they say
  
  > If found to be complete, whether single-copy or duplicated, the BUSCO
  > matches have scored within the expected range of scores ...
  
  but again, I don't understand what the score actually represents. I am even not sure if greater the better or visa reverse. Does anybody know what the score is?
  
  ```
  # BUSCO version is: 4.0.2 
  # The lineage dataset is: insecta_odb10 (Creation date: 2019-11-20, number of species: 75, number of BUSCOs: 1367)
  # Busco id      Status  Sequence        Gene Start      Gene End        Score   Length
  47at50557       Complete        scf1:20448-42284    20448   42284   4607.1  3554    https://www.orthodb.org/v10?query=47at50557     Immunoglobulin-like domain
  547at50557      Complete        scf2:9780-23590    9780    23590   2743.8  1555    https://www.orthodb.org/v10?query=547at50557    protein unc-80 homolog
  755at50557      Complete        scf3:9036-28083    9036    28083   3149.9  2206    https://www.orthodb.org/v10?query=755at50557    SRCR-like domain
  
  ```
  
  **Tags:** busco
  
  > **Comments:**
  > **username_1**: Interesting question, its not immediately obvious I definitely agree  
  > **username_2**: I don't think any of the guys from the Zdobnov lab are on this site yet, but do raise an issue on gitlab https://gitlab.com/ezlab/busco  
  > **username_2**: i recall that the bitscore cutoffs are HMMER3 thresholds that are tailored for each individual profile (i.e. model-specific), but since i never worked on BUSCO i might be wrong  
  > **username_0**: Thanks folks. If you are right about HMMER, then it is "A HMMER bit score is the log of the ratio of the sequence’s probability according to the profile (the homologyhypothesis) over the null model probability (the non-homology hypothesis)."  
  > **username_0**: I might as well invite username_3 Seppey, I think it would be healthy to have him around :-).  
  > **username_0**: @username_2 There you go, we got now! ^^  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-03-16. Score: 3 | Accepted answer
  
  You are correct, it is the score of the candidate protein against the BUSCO profile hmm assessed by hmmer. If it passes a threshold, it is validated as being that BUSCO gene. The threshold is defined for each profile based on the score of the species used to produce the profile. It can be found in `name_odb10/scores_cutoff`. And yes, the higher the better.
  
  > **Comments:**
  > **username_0**: Welcome, username_3! And thanks for the answer.  
  
  ---
  
  