fitD



NAME

     fitD - fit one sequence into another, reporting  their  dis-
     tance


SYNOPSIS

     fitD  db file2 mismatch alpha beta [ flags ]


DESCRIPTION

     fitD finds the best distance alignment between the sequences
     in  db  and the sequence in file2, given a particular set of
     scoring parameters.

     The scoring parameters are all integer values, and all posi-
     tive.   The parameters mismatch, alpha and beta are added to
     the score; match has a score of zero.

     mismatch  the amount to add for a mismatch.

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

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


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

     The format of sequence files db and file2  is  our  standard
     format,  the  Pearson/FASTA  format.   The first line is the
     sequence name, and should be used as a description.   Subse-
     quent  lines contain the sequence to be used.  The sequences
     themselves may contain blanks, returns, and other whitespace
     for  readability.   The  sequence terminates at end-of-file,
     `>' is read to begin a new sequence  in  the  FASTA  format.
     Only multiple sequences in the first file will be processed.


REFERENCES

     P.H. Sellers.  "On the theory and computation of  evolution-
          ary  distances".   SIAM Journal of Applied Mathematics,
          26 (1974) 787-793.

     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),  mfitD(1),  f
itS(1),  mfitS(1),   pfitS(1),
     sequence-file(5).