pfitS



NAME

     pfitS - fit a profile sequence into an ordinary sequence.


SYNOPSIS

     pfitS  db profile match mismatch alpha beta [ flags ]


DESCRIPTION

     pfitS finds the best alignment between the profile specified
     in profile-file and the sequence in file.

     profile   the file containing profile information,  where  a
               separate  match  score is assigned for each letter
               in each position of a sequence.  This differs from
               the penalty matrix versions (see the matrix option
               below), where one score is  assigned  to  a  given
               letter  match  regardless  of  its position in the
               sequence.  Profile files have a suffix of  ".pro";
               they  are  specified  without  this extension (for
               example,  "globins.pro"  is  specified  simply  as
               "globins").  For more information on the format of
               a profile file, see profile(5).

     The format of the sequence file db is our  standard  format,
     the  Pearson/FASTA  format.   The first line is the sequence
     name, and should be used as a description.  Subsequent lines
     contain  the  sequence to be used.  The sequences themselves
     may contain blanks, returns, and other whitespace for reada-
     bility.   The  sequence terminates at end-of-file, or if `>'
     is read, beginning a new sequence in FASTA format.  Multiple
     sequences in this file will be processed.

     The scoring parameters are all integer values, and all posi-
     tive.   The  parameters  mismatch,  alpha  and beta are sub-
     tracted from the score; match is added to the score.

     match     the score for aligning identical letters.

     mismatch  the amount to subtract for a mismatch.

     alpha     the amount to subtract for the first letter of  an
               insertion or deletion sequence (indel).

     beta      is the amount to subtract for  subsequent  letters
               in  an  indel.   For  example, if there is a five-
               letter indel, k = 5, then alpha + beta * ( k - 1 )
               =  alpha  + beta * (4) will be subtracted from the
               score.

     flags     See  manual  page  seqaln-intro  (1)  for  a  full
               description of optional flags.



REFERENCES

     P. Sellers. The theory and computation of evolutionary  dis-
          tances:   pattern recognition.  J. Algorithms, 1 (1980)
          359-373.

     M.S. Waterman and M. Perlwitz. "Line geometries for sequence
     comparisons.  Bull. Math. Biol., 1984.  46:567-77.

     M.S. Waterman.  Introduction to Computational Biology: Maps,
     sequences  and  genomes. Chapman & Hall. London: 1995.  ISBN
     0-412-99391-0.


SEE ALSO

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