107 lines
2.7 KiB
Text
107 lines
2.7 KiB
Text
.TH ted 1L "July 1991" "MRC LMB" "LOCAL"
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.SH NAME
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ted \- trace editor
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.SH SYNOPSIS
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.B ted
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[(
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.B -ABI\||\|-ALF\||\|-plain
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)
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.I tracefilename
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[
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.B -baseNum
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.I number
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]
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.B [
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.B -mag
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.I number
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( 1 to 100 )
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]
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.B [
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.B -bottom
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.I number
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(1(true) or 0(false))
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.B ]
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.B [
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.B -astring
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.I nucleotide-string
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]]
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.B [
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.B -enzyme
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.I 5' cutting sequence
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]
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.B [
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.B -raw
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.I filename
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(to be placed at head of xdap compatible .seq file)
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.B ]
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[
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.B -output
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.I outputfilename
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]
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.SH DESCRIPTION
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.B ted
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is a simple prototype editor for traces produced from automatic
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sequencing machines. It allows the traces (from the ABI
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or ALF sequencing machines) produced to be
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displayed along with the machines interpretation of these into
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bases and an initially identical sequence which can be edited
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by the user. A cutoff region can be defined at both ends. The
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edited and clipped list of bases can then be written out.
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.LP
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When initially run,
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.B ted
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displays the trace file
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.I tracefilename
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(if given) of the specified format centered on the base number
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.I baseNum
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(if given). If no file is provided,
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.B ted
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initially displays nothing.
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.LP
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The display consists of
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the control panel and the synchronized view of the base position
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information, original and edited sequence data,
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and graphical representation of the trace (with each nucleotide's trace
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being represented by a different color). The control
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panel allows the user to read in new trace files (in either
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bottom or top strand orientation)
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as well as to search for a string of nucleotides or a certain base position.
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The information button brings up signal strength and average spacing for
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ABI files.
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Scroll bars allow the user to adjust the magnification of or scroll through
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the sequence and trace data. The user may also choose to change the vertical
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magnification of the trace data. Further, sequence on the head (vector)
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or tail (uncertain data) of the sequence may be ``cutoff''
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using the adjust left and right cutoff buttons. Bases can be inserted,
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deleted, or replaced as with
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any ordinary word-processor in the sequence data window. Finally, the
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sequence may be written to an ascii file using the output button on
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the control panel. The output filename is specified in a dialogue,
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but a default value of inputfilename.seq is provided or the default value
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can be given with the
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.I outputfilename
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argument.
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.LP
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A simple help system is provided.
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.SH FILES
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.PD 0
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.TP 20
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.B ted.help
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Text provided in the help window.
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.TP
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.B /usr/lib/X11/app-defaults/Xted
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Default application resources.
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.SH ENVIRONMENT
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.TP 20
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.SB XFILESEARCHPATH
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Specifies the locations where
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.B ted.help
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is sought.
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If this is not defined,
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.B ted.help
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must be in the
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.B /usr/lib/X11/app-defaults
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directory.
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.SH AUTHORS
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Tim Gleeson, LaDeana Hillier, Simon Dear.
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