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Table 4 Comparative Tests. Comparative tests of YASS vs b12seq (NCBI BLAST 2.2.6). Reported execution times have been obtained on a Pentium IV 2.4 GHz computer.

From: Improved hit criteria for DNA local alignment

sequence 1 sequence 2 time (sec) # align. # ex. align. ex. align. length
name size name size Y. B. Y. B. Y. B. Y. B.
S.sp. 3.6 M.t. 4.4 122 148 494 310 130 27 29145 7970
S.sp. 3.6 C.g. 3.3 161 163 578 369 168 63 37310 30138
S.sp. 3.6 Y.p. 4.6 156 253 901 617 186 54 39354 19994
S.sp. 3.6 V.p. 3.3 164 167 940 465 349 60 65788 28883
M.t. 4.4 C.g. 3.3 211 542 1851 1265 397 160 102103 80012
M.t. 4.4 Y.p. 4.6 168 255 738 515 197 86 44348 23361
M.t. 4.4 V.p. 3.3 72 69 498 295 171 30 36474 12021
C.g. 3.3 Y.p. 4.6 130 161 962 640 186 45 34538 11277
C.g. 3.3 V.p. 3.3 95 93 1109 687 197 72 42009 21575
Y.p. 4.6 V.p. 3.3 149 217 2900 1953 622 264 186585 110352
  1. C.g: Corynebacterium glutamicum ATCC 13032,
  2. M.t: Mycobacterium tuberculosis (CDC1551),
  3. S.sp.: Synechocystis sp. PCC 6803,
  4. S.sp.: Vibrio parahaemolyticus RIMD 2210633 chr I,
  5. Y.p.: Yersinia pestis KIM