# NBA: Near-optimal Block Alignment

Please Input the First Sequence: S1=

e.g. bacddb
(Class Type: Characters of Set Symbol.)

Please Input the Second Sequence: S2=

e.g. abdcd
(Class Type: Characters of Set Symbol.)

Please Input the Symbols that Are Used in S1,S2: Symbol=

e.g. abcd
(Class Type: English Alphabets.)

Please Input the Score Matrix: Score Matrix=

e.g.
 - a b c d - -10000 -1 -1 -1 -1 a 4 1 0 2 b 3 0 -2 c 2 1 d 1
= -10000,-1,-1,-1,-1,4,1,0,2,3,0,-2,2,1,1
(Class Type: Matrix of Integers with size |Symbol+1|X|Symbol+1|, Upper Triangle Only.)

Please Input the Threshold of the Near-optimal: Near=

e.g. 2
(Class Type: Integers that Equal or Greater Than 0. )

Please Input the Threshold when Judging Blocks: Tau=

e.g. 0
(Class Type: Float Numbers.)

Block Color Setting:
 Red Orange Yellow Green Blue Indigo Violet White
 Red Orange Yellow Green Blue Indigo Violet White  > Tau Red Orange Yellow Green Blue Indigo Violet White  = Tau Red Orange Yellow Green Blue Indigo Violet White  < Tau

## Reference:

### Symbol Set of of Proteins

 A C D E F G H I K L M N P Q R S T V W Y

### PAM250 Score Matrix

 -99999 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 -2 2 -2 0 0 -4 1 -1 -1 -1 -2 -1 0 1 0 -2 1 1 0 -6 -3 12 -5 -5 -4 -3 -3 -2 -5 -6 -5 -4 -3 -5 -4 0 -2 -2 -8 0 4 3 -6 1 1 -2 0 -4 -3 2 -1 2 -1 0 0 -2 -7 -4 4 -5 0 1 -2 0 -3 -2 1 -1 2 -1 0 0 -2 -7 -4 9 -5 -2 1 -5 2 0 -4 -5 -5 -4 -3 -3 -1 0 7 5 -2 -3 -2 -4 -3 0 -1 -1 -3 1 0 -1 -7 -5 6 -2 0 -2 -2 2 0 3 2 -1 -1 -2 -3 0 5 -2 2 2 -2 -2 -2 -2 -1 0 4 -5 -1 5 -3 0 1 -1 1 3 0 0 -2 -3 -4 6 4 -3 -3 -2 -3 -3 -2 2 -2 -1 6 -2 -2 -1 0 -2 -1 2 -4 -2 2 -1 1 0 1 0 -2 -4 -2 6 0 0 1 0 -1 -6 -5 4 1 -1 -1 -2 -5 -4 6 0 -1 -2 2 -4 2 1 -1 -2 -3 3 0 -5 -3 4 -6 -2 17 0 10