Manual Reference Pages - ALIGN (1)
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
align [ -f # -g # -O filename -m # -s
SMATRIX -w # ] sequence-file-1 sequence-file-2
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
align weights end gaps, so that an alignment of the form
will have a higher score than:
align0 uses the same algorithm, but does not weight end gaps. Sometimes this can
have surprising effects.
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
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:
Penalty for the first residue in a gap (-12 by default).
Penalty for additional residues in a gap (-2 by default).
Sends copy of results to "filename".
(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.
(SMATRIX) the filename of an alternative scoring matrix file or "250" to use the
(LINLEN) output line length for sequence alignments. (normally 60,
can be set up to 200).
align program in interactive mode. The program will prompt for
the file name for the first sequence and the second sequence.
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
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
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