Staden Package "Pregap4" beta test

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Jul 9 06:47:38 EST 1998

We are pleased to announce a beta test version of Pregap4 (a graphical
replacement for the Pregap program). A web page describing Pregap4
will appear shortly (if it's not there already) at.


The README file from the distribution follows.


Pregap4 version 1.0, beta release 1
Last updated: 9th July 1998.

IMPORTANT: Please read the following before using this software.

The Pregap4 program, including it's sources, binaries, and documentation, is
Copyright 1998 Laboratory of Molecular Biology, MRC.

This beta release is a test release only and should not be considered public
domain software. It is part of the Staden Package. It comes under the same
licence agreement as the Staden Package.

MRC grants permission to use Pregap4 to institutions currently holding a valid
Staden Package licence.

In return for making this available we wish to receive feedback (both positive
and negative) on this work so that we can make the final release a better
tool. Please send mail on Pregap4 to jkb at mrc-lmb.cam.ac.uk.

What is it?

Pregap4 is a program to perform a series of pre-processing steps that are
required before sequence assembly. These processes include file type
conversion, base calling and base confidence assignment with phred, sequence
quality clipping, vector clipping (both sequencing vector (eg m13) and prior
cloning vectors (eg cosmid)), screening (eg for E.Coli contamination), trace
viewing and editing, repeat detection and point mutation detection. It can
also assemble the data and enter it into a Gap4 database using a variety of
assembly engines (not included): cap2, gap4, fakII, and phrap.

Each of these processes is a small separate program which may be a Staden
Package program or an external program. For example screening could be done
with the Staden Package "screen_seq" program or using "blast".

Pregap4 can run using a GUI for easy configuration, or as a non graphical
batch program for automated processing.

What do I need to run it?

Pregap4 requires the Staden Package, ideally the 1998.0 release. (We haven't
tested it on older releases.) You may also wish to obtain some of the other
non-Staden programs that it can make use of, such as blast and phred.

The distribution includes prebuilt binaries for Digital Unix 4.0, Solaris 2.5,
Irix 5.3/6.3 and Linux 2.0 (x86). Sources for the tcl components are included,
but not for the C parts.

Where do I get it from?

It's available as a gzipped tar file from the following ftp site. There are
four gzipped tar files. Download the one appropriate for your system type.


How do I install it?

To install, just uncompress and extract the tar file. This will create a
pregap4-1.0b1 directory. Eg:

	gzip -cd pregap4-1.0b1.alpha.tar.gz | tar xvf -

How do I use it?

See the files in the docs subdirectory. The "pregap4.ps" is a PostScript
document containing the current Pregap4 documentation. This is not yet
complete, but we will make the complete documentation available soon.
Alternatively see the pregap4_toc.html file for an HTML copy of the

To run pregap4, just run the pregap4 program contained in the top level
directory created by the installation (.../somewhere/pregap4-1.0b1/pregap4).

Note that some features require the newest Staden Package release (1998.0)
and/or require programs from other authors. Eg the phrap assembly support.


It is important for the development of Pregap4 to receive feedback from users.
If you find a problem and do not report it, then it probably will not be
fixed. We would also like to hear suggestions for additional features (even if
they're listed on our 'to do' list).
Please send all comments to jkb at mrc-lmb.cam.ac.uk.

Known problems / Things to do

*	Improve diagnostic text output. Eg acknowledgement that certain tasks
	have happened.

*	Provide a simple mode containing less dangerous controls. Eg no
	"select modules" mode. Perhaps a "wizard" interface?

*	Improve cross_match support. Eg for cloning vector removal, screening
	and rejecting sequences, creating tags.

*	Add an ordering check to select modules to prevent impossible module

*	RepeatMasker interface.

*	Changing the colours gives lots of errors, although it does appear to

*	Link up the online help to the program.


We would like to thank John Peden for testing of the earlier (and buggier)
Pregap4 releases.
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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