Table 1

Programs and parameters used

ID

Word size1

Parameters2


MBc16

MegaBlast

16

-r 1 -q -1 -X 40 -W 16

MBc12

MegaBlast

12

-r 1 -q -1 -X 40 -W 12

MBc11

MegaBlast

11

-r 1 -q -1 -X 40 -W 11

MBc9

MegaBlast

9

-r 1 -q -1 -X 40 -W 9

MBc8

MegaBlast

8

-r 1 -q -1 -X 40 -W 8

MBd21

MegaBlast

11/21

-t 21 -W 11 -q -3 -r 2 -G 5 -E 2 -N 2

MBd18

MegaBlast

11/18

-t 18 -W 11 -q -3 -r 2 -G 5 -E 2 -N 2

MBd16

MegaBlast

11/16

-t 16 -W 11 -q -3 -r 2 -G 5 -E 2 -N 2

BZd1

Blastz

12/19

K = 4500, L = 4500, M = 50

BZd2

Blastz

12/19

K = 2200, L = 2200, M = 50

BZc1

Blastz

8

K = 2500 L = 2500 M = 50 T = 0

PH

PatternHunter

11/18

-db 0 -mi -mj -b 2 -N 1


1For discontiguous searches the number of matches is listed first followed by the length of the match seed.

2All MegaBlast searches were run with -D 3 -U T -F 'm D'. No score filter was set to allow for subsequent filtering of matches based on scores.

Ratnakumar et al. BMC Genomics 2010 11:458   doi:10.1186/1471-2164-11-458

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