trlocalS



NAME

     trlocalS - look for tandem repeats of a specified pattern in
     a sequence


SYNOPSIS

     trlocalS  db pattern match mismatch alpha [ flags ]


DESCRIPTION

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

     The scoring parameters are all integer values, and all posi-
     tive.  The parameters mismatch and alpha are subtracted 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  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),  mtrlocalS
(1), pvlocalS(1), mpvlocalS(1), sequence-
     file(5).