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Table 2 Performance of PanGEA-BlastN with the 454-platform using the recommended settings.

From: PanGEA: Identification of allele specific gene expression using the 454 technology

tag-to-gene mapping1
   normal mode Intron mode
L2 s3 a4 c5 w6 n7 i8 t9 a4 c5 w6 n7 i8 t9
  100 126 997 1 2 6 10 111 993 5 2 63 10
100 95 95 932 6 62 0 11 104 952 6 42 11 11
  90 42 408 13 579 0 4 35 450 10 540 0 5
  100 86 993 5 2 87 34 108 991 8 1 206 40
200 95 88 988 8 4 88 38 91 994 5 1 170 41
  90 90 953 5 42 44 37 78 885 13 102 75 36
  100 114 986 10 4 211 84 94 996 3 1 407 90
300 95 86 988 10 2 188 81 102 990 6 4 354 95
  90 103 984 8 8 162 85 99 992 7 1 263 93
  100 74 994 4 2 312 128 85 988 7 5 574 153
400 95 87 986 12 2 300 137 79 981 13 6 499 153
  90 78 986 14 0 250 150 85 993 4 3 366 151
tag-to-genome mapping10
  100 32 1000 0 0 11 11 21 998 1 1 42 10
100 95 27 973 2 25 1 14 23 984 2 14 24 22
  90 14 399 4 597 0 14 11 337 13 650 1 4
  100 31 997 3 0 93 59 25 994 6 0 190 55
200 95 31 993 7 0 82 49 20 995 5 0 154 51
  90 20 961 1 38 42 45 12 956 1 43 99 47
  100 26 998 2 0 214 94 27 997 3 0 341 107
300 95 16 998 2 0 178 96 21 995 5 0 285 113
  90 23 972 9 19 151 99 21 989 10 1 250 102
  100 21 999 1 0 328 194 20 998 2 0 496 181
400 95 15 998 2 0 287 144 23 993 7 0 422 178
  90 19 996 4 0 260 168 20 992 8 0 400 168
  1. Values were calculated for mapping 1000 randomly excised ESTs, either to the genes or to the whole genome of D. melanogaster
  2. 1 settings: word length 11; minimum diagonal 3; low complexity threshold 10; homopolymer Smith-Waterman algorithm; no maximum intron length
  3. 2 length of the tags in bp
  4. 3 similarity of the tag with the target sequence in percent
  5. 4 ambiguous mapping results; min score difference for unambiguous best hit 12
  6. 5 correctly mapped tags (including ambiguous results containing the correct hit)
  7. 6 wrongly mapped tags (including ambiguous results not containing the correct hit)
  8. 7 no hit identified
  9. 8 number of long gaps (> 50 bp), putative introns
  10. 9 mapping time in seconds, without the time required for constructing the word hash-table
  11. 10 settings as above, only the maximum intron length was set to 5000 bp