text: user12579: I am trying to do a synteny analysis using MCScanX. As per requirement I have done all by all blast between two sets of protein from two closely related species. And also prepared the gff file. The file formats are as follows:
  cyp_dan.blast
  NP_001347641.1  XP_042591522.1  78.31   166     32      1       1       166     1       162     5e-91   267
  NP_001347641.1  XP_042577882.1  60.24   166     62      2       1       166     1       162     4e-63   196
  .
  .
  XP_704272.2     XP_018953536.1  31.03   87      59      1       275     360     90      176     8e-07   50.4
  XP_704272.2     NP_001005958.2  33.33   63      38      1       273     331     38      100     1e-06   48.9
  XP_704272.2     XP_018969808.1  31.33   83      56      1       275     356     91      173     2e-06   49.3```
  
  cyp_dan.gff
  NC_056572.1     gene-LOC1221465.1       2966    7093
  NC_056572.1     id-LOC122146575.1       2966    3166
  NC_056572.1     id-LOC122146575.1       3246    3357
  .
  .
  NC_002333.2     gene-trnP;Dbxre.1       16527   16596
  NC_002333.2     rna-trnP;Parent.1       16527   16596
  NC_002333.2     exon-trnP-1;Par.1       16527   16596
  
  cmdline: /home/software/MCScanX/MCScanX cyp_dan
  Output:
  ############### Parameters ###############
  # MATCH_SCORE: 50
  # MATCH_SIZE: 5
  # GAP_PENALTY: -1
  # OVERLAP_WINDOW: 5
  # E_VALUE: 1e-05
  # MAX GAPS: 25
  ############### Statistics ###############
  # Number of collinear genes: 0, Percentage: 0.00
  # Number of all genes: 108556
  ##########################################
  
  Here, both of the species are from same family since there is no chance to have "zero collinear gene".
  
  user96: I'm not familiar with the MCScanX tool, but I see two potential issues that are worth investigating.
  
  The cyp_dan.gff file does not look like GFF or any of its common variants (GFF3, GTF, etc.). Again, I'm unfamiliar with MCScanX, so I don't know precisely how its wants the input data formatted. But if it wants a GFF file, I would double-check to make sure that what you have matches what the tools expects/requires.
  
  The gene/protein IDs in the cyp_dan.gff file do not seem to match the query or subject IDs in the cyp_dan.blast file. No tool is going to be able to find collinear adjacent genes if the IDs in the BLAST results don't match the IDs in the gene annotations.
  
  
  
original_text: 12579: <p>I am trying to do a synteny analysis using MCScanX. As per requirement I have done all by all blast between two sets of protein from two closely related species. And also prepared the gff file. The file formats are as follows:</p>
  <p>cyp_dan.blast</p>
  <pre><code>NP_001347641.1  XP_042591522.1  78.31   166     32      1       1       166     1       162     5e-91   267
  NP_001347641.1  XP_042577882.1  60.24   166     62      2       1       166     1       162     4e-63   196
  .
  .
  XP_704272.2     XP_018953536.1  31.03   87      59      1       275     360     90      176     8e-07   50.4
  XP_704272.2     NP_001005958.2  33.33   63      38      1       273     331     38      100     1e-06   48.9
  XP_704272.2     XP_018969808.1  31.33   83      56      1       275     356     91      173     2e-06   49.3```
  
  cyp_dan.gff
  NC_056572.1     gene-LOC1221465.1       2966    7093
  NC_056572.1     id-LOC122146575.1       2966    3166
  NC_056572.1     id-LOC122146575.1       3246    3357
  .
  .
  NC_002333.2     gene-trnP;Dbxre.1       16527   16596
  NC_002333.2     rna-trnP;Parent.1       16527   16596
  NC_002333.2     exon-trnP-1;Par.1       16527   16596
  
  cmdline: /home/software/MCScanX/MCScanX cyp_dan
  Output:
  ############### Parameters ###############
  # MATCH_SCORE: 50
  # MATCH_SIZE: 5
  # GAP_PENALTY: -1
  # OVERLAP_WINDOW: 5
  # E_VALUE: 1e-05
  # MAX GAPS: 25
  ############### Statistics ###############
  # Number of collinear genes: 0, Percentage: 0.00
  # Number of all genes: 108556
  ##########################################
  </code></pre>
  <p>Here, both of the species are from same family since there is no chance to have &quot;zero collinear gene&quot;.</p>
   96: <p>I'm not familiar with the MCScanX tool, but I see two potential issues that are worth investigating.</p>
  <ol>
  <li><p>The <code>cyp_dan.gff</code> file does not look like GFF or any of its common variants (GFF3, GTF, etc.). Again, I'm unfamiliar with MCScanX, so I don't know precisely how its wants the input data formatted. But if it wants a GFF file, I would double-check to make sure that what you have matches what the tools expects/requires.</p>
  </li>
  <li><p>The gene/protein IDs in the <code>cyp_dan.gff</code> file do not seem to match the query or subject IDs in the <code>cyp_dan.blast</code> file. No tool is going to be able to find collinear adjacent genes if the IDs in the BLAST results don't match the IDs in the gene annotations.</p>
  </li>
  </ol>
  