msrlocalS



NAME

     msrlocalS - finds self-repeats in a sequence, using similar-
     ity scoring with a penalty matrix.


SYNOPSIS

     msrlocalS  file matrix csub alpha beta [ flags ]


DESCRIPTION

     msrlocalS looks for  self-repeats  of  subsequences  in  the
     sequence  in file (given a particular set of scoring parame-
     ters), using a penalty  matrix,  and  reports  those  repeat
     alignments  having  a  cutoff score of at least # if the -c#
     option is specified, or with # of  repeat  local  alignments
     with highest scores if the -n# option is specified.

     The scoring parameters are all integer values, and all posi-
     tive.


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


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

     The format of the sequence file file is our standard format,
     or 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 in our format or `>' is read in the Pearson format.


REFERENCES

     T.F. Smith and M.S.  Waterman.   "Identification  of  Common
          Molecular Subsequences".  Journal of Molecular Biology,
          147, (1981) 195.

     M.S. Waterman and M. Eggert.   "A  New  Algorithm  for  Best
          Subsequence  Alignments  with  Application to tRNA-rRNA
          Comparisons".  Journal of Molecular Biology 197  (1987)
          723-728.

     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),  srlocalS(1),  trlo-
     calS(1),  mtrlocalS
(1),  pvlocalS(1), <
STRONG>mpvlocalS(1), penalty-
     matrix(5), sequ
ence-file(5).