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Table 2 Results of a set of 1000 simulated sequences with different mutation rates.

From: Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

  Number of being rejecteda IGHD IGHD IGHJ
   Wrong pickupsb Accuracy (%)c Missingd Wrong pickups Accuracy (%) Wrong pickups Accuracy (%)
Ab-origin 0 30 97.0 7 113 88.0 19 98.1
IMGT\V-QUEST 0 30 97.0 29 147 82.4* 44 95.6*
SoDA 0 87 91.3* 3 161 83.6* 83 91.7*
JOINSOLVER 26 161 81.3* 9 214 75.1* 46 92.8*
VDJsolver 97 80 82.3* 73 86 74.4* 35 86.8*
iHMMune-align 68 67 86.5* 22 111 79.9* 37 89.5*
  1. The numbers represent the results from six programs. A wrong pickup means that the identified gene segment was not the one we used exactly in simulation.
  2. a Number of the rearranged sequences cannot be deciphered by the tool due to various reasons. Some tools give the explanation for rejection, i.e. JOINSOLVER could not well define the CDR3 region [15]; iHMMune-align is not intended for gaps in IGHV and short length of IGHV [17].
  3. b Number of the wrong pickups among the sequences already been deciphered.
  4. c Accuracy = 1-(wrong pickups+ number of missing+ number of being rejected)/1000
  5. d Number of the sequences already been deciphered by the tool but didn't find the IGHD alignment because of respective restrictions.
  6. * Demonstrate that the accuracy of Ab-origin is significantly higher than that of the tool.