108 lines
4.4 KiB
Text
108 lines
4.4 KiB
Text
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reform update 3 Feb 94
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NAME
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reform - reformats multiply-aligned sequences for printing.
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SYNOPSIS
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reform [-gpcnm] [-fx] [-sn] [-ln] [file {ralign only}]
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or
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ralign file parameters | reform [-gpcn] [-sn] [-ln] file
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DESCRIPTION
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g Gaps are to be represented by dashes (-).
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p Bases which agree with the consensus are
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represented by periods (.).
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c Positions at which all sequences agree are
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capitalized in the consensus.
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n Sequence data is nucleic acid. Protein default
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fx Specify input file format, where x is
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r:RALIGN (default) p:PEARSON i:MBCRR-MASE (Intelligenetics)
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m Input file contains multiline format sequences already aligned,
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as opposed to ralign output. This option is obsolete, and is
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equivalent to -fp.
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ln The output linelength is set to n.
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Default is 70.
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sn numbering starts with n (default=0)
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file Sequence file as described in ralign docu-
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mentation. reform needs to re-read the
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sequence file read by ralign to get the
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names of the sequences, which ralign ignores.
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This filename is only included for ralign output.
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If -m is set, file is ignored, and sequence names
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must be read from the input.
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Note that positions in the consensus at which no nucleotide is in the
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majority are represented by n's (for nucleic acids) or x's (for proteins),
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rather than periods, as in ralign.
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Gaps in the input sequences may be represented by either blanks or dashes.
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INPUT FILE FORMATS
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(a) ralign (default, -fr)
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As described in ralign documentation, the input file (which is assumed to
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be ralign output) must have each sequence on a single long line. All
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characters on a given line will be included in the alignment. All lines
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must be exactly the same length. For example, if ralign had been read
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sequence from a file called 'allcab.seq' and written output to 'allcab.ral',
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the following command might be used:
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reform allcab.seq <allcab.ralign >allcab.ref
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(b) Pearson (-fp, -m)
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Compatible with sequence files used by Pearson's fasta programs as shown:
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>name1
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sequence1
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>name2
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sequence2
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...
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>namen
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sequencen
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Sequences may run over many lines and line length does not have to be
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uniform. However, both dashes ('-') and blanks (' ') will be read in
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as gaps in the alignment. A right arrow (>) at the beginning of a line
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indicates the name line at the beginning of a new sequence.
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Any line beginning with a semicolon (';') will be considered a comment,
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and will be ignored.
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(c) MBCRR-MASE (Intelligenetics) (-fi)
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Compatible with .mase files produced by MBCRR's mase and pima programs,
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which use the Intelligenetics format as shown:
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;one or more comment lines
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name1
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sequence1
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;one or more comment lines
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name2
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sequence2
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...
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;one or more comment lines
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namen
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sequencen
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Sequences may run over many lines and line length does not have to be
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uniform. However, both dashes ('-') and blanks (' ') will be read in
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as gaps in the alignment. Each sequence MUST begin with at least one
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comment line. When a comment line is encountered, that signals the
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beginning of a new sequence. The first line after the comment is read
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as the name, and the sequence begins on the next line after that.
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SEE ALSO ralign, mase
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AUTHOR
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Dr. Brian Fristensky
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Dept. of Plant Science
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University of Manitoba
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Winnipeg, MB Canada R3T 2N2
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Phone: 204-474-6085
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FAX: 204-261-5732
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frist@cc.umanitoba.ca
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REFERENCE
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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