text: user57: The BUSCO _full_table.tsv output has scores per gene (an example bellow).
  In the original publication, authors just mention a condition to satisfy a bitscore, but I could not find what the bitscore actually is. In the use guide 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
  
  
  user7413: 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.
  
original_text: 57: <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>
   7413: <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>
  