A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Algorithm 1

IncrementalPartialAlign 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;

if   sr  >  t  then

  exit;    // no deletion

else

 sr is SWSR of 𝑟 and [𝑞₀, 𝑞_𝑚];

 iteration = 1;

 f = m + iteration;

  while  sr  >  t

    sr is SWSR of 𝑟 and [𝑞₀, 𝑞_𝑓];

    iteration ++;

  end while

   return  f;

end if