Advances in Bioinformatics

Research Article

Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases

Algorithm 7

goo2( ).
(1) posi a list of positions of a specified qmer in D
 ( where corresponds to position of sequence )
(2) mut a list of positions of qmers in D that mismatch this qmer by either 1 or 2 characters
  (depending on the filtration algorithm using this function)
(3) for   to length( )  do
(4)  for   to length( )  do
(5)   if     then
(6)     list of -mers generated from the extension of the in position
(7)     list of -mers generated from the extension of the in position
(8)    for   to length( )  do
(9)     for   to length( )  do
(10)     if     then
(11)       mark the as non-unique
(12)     end if
(13)     end for
(14)    end for
(15)   end if
(16)  end for
(17)  for   to length( )  do
(18)   if     then
(19)     list of -mers generated from the extension of the in position
(20)     list of -mers generated from the extension of the in position
(21)    for   to length( )  do
(22)     for   to length( )  do
(23)     if     then
(24)       mark the as non-unique
(25)     end if
(26)     end for
(27)    end for
(28)    end if
(29)  end for
(30) end for