102 lines
2.8 KiB
Text
102 lines
2.8 KiB
Text
.TH staden 1L "November 1991" "MRC LMB" "LOCAL"
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.SH NAME
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staden, xstaden \- sequence analysis suite
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.SH DESCRIPTION
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.I staden
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is a suite of programs for sequence analysis. Currently available are
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.I mep,
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.I nip,
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.I pip,
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.I sap,
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.I sip,
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.I nipl,
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.I pipl,
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.I and sipl.
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These all run under the SUN X11
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.I xterm
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Tektronics terminal emulator, but also work with the VT640 terminal
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and the VersaTermPro and MS-Kermit emulators if they login to a SUN.
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.PP
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.I xstaden
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is the same set of programs, named
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.I xmep,
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.I xnip,
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.I xpip,
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.I xsap,
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.I xdap,
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and
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.I xsip,
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which run directly under X providing a convenient user interface,
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including resizable output and pull-down menus. All these programs
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accept the standard X arguments. The library searching programs
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nipl, pipl and sipl are only available in xterm form.
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.PP
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Sequence library access is provided for the format as distributed
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on CDROM by EMBL. The CDROM contains the EMBL nucleotide library and
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the SWISSPROT protein library. The libraries can be left on the
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CDROM or transferred to hard disk.
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.PP
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The programs also provide an interface to the PROSITE protein motif
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library.
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.PP
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Some initialisation is required in order to use the package. csh users
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should insert the following in their .login files:
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.IP
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setenv STADENROOT /home/BioSW/staden
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.IP
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source $STADENROOT/staden.login
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.LP
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Users of the Bourne shell, sh, should insert the following in
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their .profile:
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.IP
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STADENROOT=/home/BioSW/staden
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.IP
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export STADENROOT
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.IP
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. $STADENROOT/staden.profile
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.LP
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These initialisations will alter your shell's search path so
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that it can find the program binaries, and other files that are
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required.
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.SH ENVIRONMENT
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The following environment variables may be set in the
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user's \fI .login\fP or \fI .profile\fP file:
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.TP 20
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.BI STADENROOT= /home/BioSW/staden
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This must be set in the user's initialisation.
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.TP 20
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.BI SEQEDT= editor
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Set the editor to be used by the package. The default is
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\fIemacs\fP.
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.SH FILES
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.PD 0
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.TP 30
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$STADENROOT/staden.login
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csh initialisation
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.TP 30
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$STADENROOT/staden.profile
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sh initialisation
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.TP 30
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$STADENROOT/tables
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Tables used by the programs
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.TP 30
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$STADENROOT/help
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Helpfiles used by the programs, documentation of the user interface
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and of each of the programs.
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.TP 30
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$STADENROOT/tables/SEQUENCELIBRARIES
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Defines the sequence libraries available, their file descriptors
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and the prompts to appear on the users screen.
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.SH AUTHOR
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Rodger Staden, MRC Laboratory of Molecular Biology, Hills Rd., Cambridge,
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CB2 2QH, UK.
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.SH BUGS
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.PP
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When using the xterm programs and in graphics input mode,
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a carriage return should not be
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entered on its own but should be preceded by some other character,
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such as SPACE, COMMA or K. If a carriage return is entered on its
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own, some garbage will (relatively) harmelssly appear on the plot.
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.PP
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General comments on the package can be sent to
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\fI<rs@uk.ac.cam.mrc-lmb>\fP
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