mtrlocalS



NAME

     mtrlocalS - look for tandem repeats of a  specified  pattern
     in a sequence using a penalty matrix


SYNOPSIS

     mtrlocalS  db pattern matrix csub alpha [ flags ]


DESCRIPTION

     mtrlocalS looks for tandem repeats of a given pattern in the
     sequence  in file (given a particular set of scoring parame-
     ters), using a penalty matrix, and reports the best score.

     matrix    is a lower-diagonal penalty matrix  with  26  rows
               and  columns,  corresponding  to the 26 letters of
               the alphabet.  This allows matrices  to  be  built
               for protein, DNA, and RNA sequences depending upon
               the letters used.  The most  common  use  of  this
               matrix  is to compare amino acid sequences in pro-
               teins, but the flexibility  of  the  matrix  input
               allows  other  types  of sequences to be compared.
               The matrix file name ends in ".mat";  this  suffix
               is  not  given.  If the matrix is not found in the
               current directory,  the  directory  given  by  the
               environment variable MATDIR will be examined.


     csub      is the lower limit for conservative substitutions,
               which  are non-matching substitutions printed with
               a `:' in alignment output.


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


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

     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.


REFERENCES

     E. Myers and W. Miller.  "Approximate  matching  of  regular
     expressions.  Bull. Math. Biol. (1989).  51:5-37.


     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), localS(1), mlocalS(1), msrlocalS(1),<
/STRONG>  srlo-
     calS(1),  trlocalS(1
),  pvlocalS(1),  mpvlocalS(1), penalty-
     matrix(5), sequ
ence-file(5).