From bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!hobbes.physics.uiowa.edu!moe.ksu.ksu.edu!unmvax!uokmax!aardvark.ucs.uoknor.edu!broe Mon Dec 16 16:13:40 EST 1991
Article: 1742 of bionet.software
Newsgroups: bionet.software
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From: broe@aardvark.ucs.uoknor.edu (Bruce Roe)
Subject: re: XDAP programs
Message-ID: <16DEC199111460522@aardvark.ucs.uoknor.edu>
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Keywords:  XDAP, Staden
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Organization: University of Oklahoma - University Computing Services
Date: Mon, 16 Dec 1991 17:46:00 GMT

Anthony Persechini writes:

>Where does one get XDAP and what machines does it run on?
>--
>ajp2o@crocus.medicine.rochester.edu

	These programs, described briefly below can be obtained from
Simon Dear and Roger Staden at the MRC, Lab. Molec. Biol., Hills Road
Cambridge, England.

        Staden's e-mail address is: RS@MRC-LMB.CAM.AC.UK

	The X-windows version of the programs run on unix boxes.  Over the
past 10 years, Staden has published many papers describing is programs which
are available for the VAX/VMS and his recent port to the SUN UNIX O/S and the
fluorescent sequencing instrument data analysis programs are described in:

   Dear, S. and Staden, R. Nucl. Acids Res.  19, 3907-3911 (1991).
   and another upcoming Nucleic Acids Research publication.

	Briefly, these programs take the ABI or Pharmacia analized data
( sequences and graphics ) and place them in a form which can be entered
into the Staden Sequence Alignment Program (SAP) [the unix version is XDAP].
	Once a contig is formed it can be edited by viewing the ABI graphic 
output and proof reading directly on the SPARCstation.  Over the past 10 
years, Staden, et al have developed a series of programs for sequence
alignment and analysis for the VAX.  They now have ported these to the 
SPARCstation and added a sequence trace editor (TED) which can deal with
the output from both ABI and Pharmacia fluorescent sequencing instruments
and an X-windows-base sequence assembly program (XDAP) which allows proof
reading from the ABI/Pharm. traces once the alignments have been made.
--bruce
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From bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!rpi!uwm.edu!bionet!GENOME.WUSTL.EDU!pg Mon Dec 16 16:16:30 EST 1991
Article: 1743 of bionet.software
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From: pg@GENOME.WUSTL.EDU (Phil Green)
Newsgroups: bionet.software
Subject: re: XDAP programs
Message-ID: <9112162104.AA12726@genome.wustl.edu>
Date: 16 Dec 91 21:04:20 GMT
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broe@aardvark.ucs.uoknor.edu (Bruce Roe) writes:
> Over the past 10 
>years, Staden, et al have developed a series of programs for sequence
>alignment and analysis for the VAX.  They now have ported these to the 
>SPARCstation and added a sequence trace editor (TED) which can deal with
>the output from both ABI and Pharmacia fluorescent sequencing instruments
>and an X-windows-base sequence assembly program (XDAP) which allows proof
>reading from the ABI/Pharm. traces once the alignments have been made.

TED was written by Tim Gleeson (originally at the MRC) and LaDeana
Hillier (at Washington University), and is described in an in-press NAR
paper by those authors. It is a standalone program (independent of
the XDAP package) which provides editing and viewing capabilities 
for individual (i.e. non-aligned) automated sequencer trace files;
parts of it were incorporated into XDAP. It only runs on SPARCstations,
under X Windows, and can be obtained for free (for research purposes)
in the US by writing to lfw@elegans.wustl.edu. 

Phil Green