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ALIGN(1)               DragonFly General Commands Manual              ALIGN(1)


NAME

       align - compute the global alignment of two protein or DNA sequences

       align0 - compute the global alignment of two protein or DNA sequences
       without penalizing for end-gaps


SYNOPSIS

       align [ -f # -g # -O filename  -m # -s SMATRIX -w # ] sequence-file-1
       sequence-file-2


DESCRIPTION

       align produces an optimal global alignment between two protein or DNA
       sequences.  align will automatically decide whether the query sequence
       is DNA or protein by reading the query sequence as protein and
       determining whether the `amino-acid composition' is more than 85%
       A+C+G+T.  align uses a modification of the algorithm described by E.
       Myers and W. Miller in  "Optimal Alignments in Linear Space" CABIOS
       (1988) 4:11-17.  The program can be invoked either with command line
       arguments or in interactive mode.

       align weights end gaps, so that an alignment of the form
            -----MACF
            SRTKIMACF
       will have a higher score than:
            MACF
            MACF
       align0 uses the same algorithm, but does not weight end gaps.
       Sometimes this can have surprising effects.

       align and align0 use the standard fasta format sequence file.  Lines
       beginning with '>' or ';' are considered comments and ignored;
       sequences can be upper or lower case, blanks,tabs and unrecognizable
       characters are ignored.  align expects sequences to use the single
       letter amino acid codes, see protcodes(1) .


OPTIONS

       align can be directed to change the scoring matrix and output format by
       entering options on the command line (preceeded by a `-' or `/' for MS-
       DOS). All of the options should preceed the file name arguments.
       Alternately, these options can be changed by setting environment
       variables.  The options and environment variables are:

       -f #   Penalty for the first residue in a gap (-12 by default).

       -g #   Penalty for additional residues in a gap (-2 by default).

       -O filename
              Sends copy of results to "filename".

       -m #   (MARKX) =1,2,3. Alternate display of matches and mismatches in
              alignments. MARKX=1 uses ":","."," ", for identities,
              consevative replacements, and non-conservative replacements,
              respectively. MARKX=2 uses " ","x", and "X".  MARKX=3 does not
              show the second sequence, but uses the second alignment line to
              display 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 or
              "250" to use the PAM250 matrix.

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


EXAMPLES

       (1)    align musplfm.aa lcbo.aa

       Compare the amino acid sequence in the file musplfm.aa with the amino
       acid sequence in the file lcbo.aa Each sequence should be in the form:
            >LCBO bovine preprolactin
            WILLLSQ ...

       (2)    align -w 80 musplfm.aa lcbo.aa > musplfm.aln

       Compare the amino acid sequence in the file musplfm.aa with the
       sequences in the file lcbo.aa Show both sequences with 80 residues on
       each output line and write the output to the file musplfm.aln.

       (3)    align

       Run the align program in interactive mode.  The program will prompt for
       the file name for the first sequence and the second sequence.


SEE ALSO

       rdf2(1),protcodes(5), dnacodes(5)


AUTHOR

       Bill Pearson
       wrp@virginia.EDU

                                     local                            ALIGN(1)

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