substitution-matrix



NAME

     substitution-matrix - format for 26 by  26-letter  substitu-
     tion matrix.


DESCRIPTION

     The substitution matrix is a lower-diagonal matrix  consist-
     ing  of  26  rows and columns.  Unused entries are typically
     filled with zeroes.  Other entries contain  a  score  to  be
     applied when a match is found.  For example, if A is matched
     with A, the score in the first row and column  is  added  to
     the  cumulative score.  If A is matched with C, the score in
     the third row and first column is added.


EXAMPLES

     The following is the beginning of a sample  matrix  for  DNA
     sequence matching.

          10
           0      0
          -2      0     10
           0      0      0      0
           0      0      0      0      0
           0      0      0      0      0      0
          -2      0      7      0      0      0     10
           0      0      0      0      0      0      0      0
           .
           .
           .

     Looking at the matches for G in the seventh row, the match G
     -A has score -2, G-C has score 7, and G-G has score 10.

     A full DNA scoring matrix for use with Genbank, for example,
     should have entries for scoring N (any) and X (any protein).
     Genbank encodes U in RNA as T; to be  safe,  if  building  a
     matrix  to compare RNA against a database, identical entries
     should be made for U and T.

     Alternatively, substitution matrices in BLAST format may  be
     used.   Thus,  as  new  matrices  are  made available in the
     NCBI's blastapp distribution, they  are  supported  by  this
     package.


SEE ALSO

     seqaln-intro(1),   mglobalS(1),    mglobalD(1),    mfitS(1),
     mfitD(1), moverS(1), mlocalS(1), msrlocalS(1), mtrlocalS(1),
     mpvlocalS(1).