fitS



NAME

     fitS - fit one sequence into another.


SYNOPSIS

     fitS  db file2 match mismatch alpha beta [ flags ]


DESCRIPTION

     fitS  finds  the  best  similarity  alignment  between   the
     sequences  in db and the sequence in file2, given a particu-
     lar set of scoring parameters.

     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.

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

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