A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Algorithm 2

BinaryPartialAlign pseudocode.

Input

reference sequence: r,

query pattern: q,

minimum sequence length: m,

threshold similarity ratio: t

Output

location(index) of deletion: f

sr = SWSR of 𝑟 and q

//SWSR stands for Smith-Waterman similarity ratio of 𝑟 and q

l is length of the query pattern;

if  sr  >  t  then

  exit ;   // no deletion

else

 i = 1;   // iteration

 f = 1/2;

 repeat

  sr1 = SWSR of 𝑟 and [𝑞₀, 𝑞_𝑓];

  sr2 = SWSR of 𝑟 and [𝑞_𝑓+1, 𝑞_𝑙];

  𝑘=1×(1/2)^(𝑖+1);

  if sr1 > t and sr2 < t then

   f = f + k;

  else if sr1 < t and sr2 > t then

   f = f - k;

  else if sr1 < t and sr2 > t then

   exit ;

  end if

  i++;

 until (sr1 ≤ t and sr2 ≤ t)

 return  f;

end if