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Table 16 Compartmentization based on local alignments computed using different methods. N1 is the number of mRNA sequences with 75% or higher coverage by alignments to any single chromosome or unplaced scaffold.N2 is the number of mRNA sequences with 75% or higher coverage by high-identity alignments to any single chromosome or unplaced scaffold. N3 is the number of sequences for which at least one compartment was identified with the minimum compartment identity of 75%. The computing time was collected on Intel Xeon 2.33 GHz/8 GB Linux box.

From: Splign: algorithms for computing spliced alignments with identification of paralogs

   MB/RM MB/WM Compart
Human 36.3 N 1 232342 (94.95%) 234565 (95.86%) 238851 (97.61%)
  N 2 224054 (91.56%) 226293 (92.48%) 229101 (93.63%)
  N 3 231939 (94.79%) 234207 (95.71%) 236928 (96.82%)
  time (min) 179 70 32
Mouse 37.1 N 1 227831 (98.44%) 228681 (95.17%) 232245 (96.65%)
  N 2 222746 (92.70%) 223704 (93.09%) 226107 (94.09%)
  N 3 226964 (94.45%) 227895 (94.84%) 230478 (95.91%)
  time (min) 372 59 29