plalign - compare two sequences for local similarity and plot the local
       sequence alignments


       lalign [-fgOmsw] sequence-file-1 sequence-file-2 [ #-of-alignments ]

       plalign [-fgmsv] sequence-file-1 sequence-file-2 [ #-of-alignments ]


       lalign  and  plalign  programs  compare two sequences looking for local
       sequence similarities.  lalign/plalign use code developed by  X.  Huang
       and  W.  Miller (Adv. Appl. Math. (1991) 12:337-357) for the "sim" pro-
       gram.  While ssearch reports only the best alignment between the  query
       sequence  and  the  library  sequence, lalign and plalign will report a
       specified number of alignments (the default  is  10)  between  the  two
       sequences  lalign  shows  the  actual  local alignments between the two
       sequences and their scores, while plalign produces a plot of the align-
       ments  that  looks  similar  to a 'dot-matrix' homology plot.  On Unix(TM)
       systems, plalign generates postscript output.

       The lalign/plalign/fasta programs use a standard text  format  sequence
       file.   Lines  beginning  with  '>'  or ';' are considered comments and
       ignored; sequences can be upper or lower case, blanks,tabs and unrecog-
       nizable characters are ignored.  lalign/plalign expect sequences to use
       the single letter amino acid codes, see protcodes(1) .


       lalign and the other programs can be directed  to  change  the  scoring
       matrix,  search  parameters, output format, and default search directo-
       ries by entering options on the command line (preceeded by a '-').  All
       of the options should preceed the file name and ktup arguments). Alter-
       nately, these options can be changed by setting environment  variables.
       The options and environment variables are:

       -f #   Penalty for the first residue a gap (-14 by default).

       -g #   Penalty for each additional residue in a gap (-4 by default).

       -m #   (MARKX)  =1,2,3.  Alternate display of matches and mismatches in
              alignments. MARKX=1 uses ":","."," ", for  identities,  conseva-
              tive  replacements,  and  non-conservative replacements, respec-
              tively. MARKX=2 uses " ","x", and "X".  MARKX=3  does  not  show
              the  second sequence, but uses the second alignment line to dis-
              play matches with a "."  for identity, or  with  the  mismatched
              residue  for  mismatches.   MARKX=3 is useful for aligning large
              numbers of similar sequences.

       -s str (SMATRIX) the filename of an alternative  scoring  matrix  file.
              For  protein sequences, PAM250 is used by default; PAM120 can be
              Normally, the values are 200, 100, and 50 for  protein  sequence
              comparisons  and 400, 200, and 100 for DNA sequence comparisons.

       -w #   (LINLEN) output line length for sequence alignments.   (normally
              60, can be set up to 200).


       (1)    lalign mchu.aa mchu.aa

       Compare  the  amino  acid  sequence in the file mchu.aa with itself and
       report the ten best local alignments.  Sequence files should  have  the

            >MCHU - Calmodulin - Human ...
            ADQLTEEQIAEF ...

       (2)    plalign qrhuld.aa egmsmg.aa  50

       Display  the  50  best local alignments of the LDL receptor (qrhuld.aa)
       with epidermal growth factor precursor (egmsmg.aa).  Plot  the  results
       on the screen.

       (3)    lalign

       Run  the  lalign  program in interactive mode.  The program will prompt
       for the name of two sequence files and  the  number  of  alignments  to


       ssearch(1), rss(1), fasta(1), protcodes(5), dnacodes(5)


       Bill Pearson

                                     local                   LALIGN/PLALIGN(1)