localS



NAME

     localS - compare two sequences to  find  best-scoring  local
     alignments.


SYNOPSIS

     localS  db file2 match mismatch alpha beta [ flags ]


DESCRIPTION

     localS finds the best local alignments between sequences  in
     db  and  the  sequence  in  file2 (given a particular set of
     scoring  parameters),  and  reports  those  non-intersecting
     local  alignments  having a score of at least a cutoff score
     of # if the -c# option is specifi ed,  or  with  #  of  non-
     intersecting 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 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.


EXAMPLES

     The examples below compare the sequence TAAAATAGAT with  the
     sequence  TAGTAGATAGTAGAT,  and  demonstrate  how  different
     choices for the scoring parameters can  produce  di ff erent
     alignments.   In both examples, only the best (i.e., highest
     scoring) alignment is requested.
          example% localS f1 f2 10 2 20 1 -n 1

          finds 7 matches and 2 mismatches beginning at position 2 in the first sequence
          and position 7 in the second sequence:

               2 AAAATAGAT
                 | | |||||
               7 ATAGTAGAT

          for a score of 10(7) - 2(2) = 66.

          example% localS f1 f2 10 2 2 1 -n 1

          finds 10 matches, 3 one-letter indels and 1 two-letter indel beginning at
          position 1 for both sequences:

               1 TA--A-A-A-TAGAT
                 ||  | | | |||||
               1 TAGTAGATAGTAGAT

          for a score of 10(10) - 3(2) - (2+1) = 91.


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),  mlocalS(1),   srlocalS(1),   msrlocalS
(1),
     trlocalS(1),    mtrlocalS(1),   pvlocalS(1),   mpvlocalS(1
),
     sequence-file(5)