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Table 3 Comparisons of the number of predicted shared transcripts (shared) and the number of predicted shared transcripts that have BLAST hits from each organism to its known transcriptome database (found) in the test on mouse against rat from Oases and from Mutual over different values of k and k-mer coverage cutoff c and over different e-value cutoffs 107 and 10−20 .

From: Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data

  mouse(10−7 )   rat(10−7 )
  Oases Mutual   Oases Mutual
k _ c shared found shared found k _ c shared found shared found
25_3 27671 26756 (97%) 35230 34011 (97%) 25_3 24489 21844 (89%) 39287 34298 (87%)
25_5 12729 12366 (97%) 14924 14520 (97%) 25_5 10092 9245 (92%) 15287 13639 (89%)
25_10 3955 3823 (97%) 4589 4465 (97%) 25_10 2994 2835 (95%) 3955 3705 (94%)
31_3 22635 22046 (97%) 25035 24396 (97%) 31_3 20917 19008 (91%) 27484 24744 (90%)
31_5 10229 10028 (98%) 11039 10825 (98%) 31_5 8398 7815 (93%) 11225 10332 (92%)
31_10 2597 2545 (98%) 2871 2815 (98%) 31_10 2013 1939 (96%) 2489 2382 (96%)
  mouse(10 −20 )   rat(10 −20 )
  Oases Mutual   Oases Mutual
k _ c shared found shared found k _ c shared found shared found
25_3 22936 22290 (97%) 28705 27881 (97%) 25_3 19282 17719 (92%) 29923 26898 (90%)
25_5 10904 10608 (97%) 12648 12336 (98%) 25_5 8242 7669 (93%) 12087 10999 (91%)
25_10 3377 3253 (96%) 3901 3790 (97%) 25_10 2510 2388 (95%) 3254 3070 (94%)
31_3 18052 17627 (98%) 20026 19567 (98%) 31_3 15835 14699 (93%) 20943 19264 (92%)
31_5 8429 8261 (98%) 9157 8964 (98%) 31_5 6623 6218 (94%) 8886 8251 (93%)
31_10 2196 2150 (98%) 2438 2386 (98%) 31_10 1681 1629 (97%) 2041 1959 (96%)
  1. The number in parentheses is the percentage of predicted shared transcripts that have BLAST hits from each organism to its known transcriptome database.