srlocalS



NAME

     srlocalS - look for self-repeats in a sequence, using  simi-
     larity scoring.


SYNOPSIS

     srlocalS  file match mismatch alpha beta [ flags ]


DESCRIPTION

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

     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 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), msrlocalS(1),<
/STRONG>  trlo-
     calS(1),  mtrlocalS
(1), pvlocalS(1), mpvlocalS(1), sequence-
     file(5).