mlocalS



NAME

     mlocalS - compare two sequences, using a penalty matrix,  to
     find best-scoring local alignments.


SYNOPSIS

     mlocalS  db file2 matrix csub alpha beta [ flags ]


DESCRIPTION

     mlocalS finds the best local alignments between sequences in
     db  and  the  sequence in file2 using penalty matrix matrix,
     along with scoring parameters  csub,  alpha  and  beta,  and
     reports  those  non-intersecting  local  alignments having a
     cutoff score of at least # if the -c# option  is  specified,
     or  #  of  non-intersecting  local  alignments  with highest
     scores if the -n# option is specified.

     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.

     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 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.


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