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Version-2000.0 Release Notes

James Bonfield, Kathryn Beal, Matthew Betts, Mark Jordan and Rodger Staden

This release has been slow to come out because we wanted it to coincide with, and be identical to, the first Windows 9X/NT release of the package. Achieving this has taken longer than planned, but has left us with the same source code for all systems, and so in a strong position for future developments. We have also given the manual a major overhaul and produced separate versions for UNIX and Windows. The different manuals include their system specific screendumps and we have also introduced alternatives for users with two button mice. (The middle mouse button may now be simulated by using the Alt key with the left mouse button.) A new "mini-manual", giving a quick (45 page) introduction to the programs, has also been written. Finally, we now also include some notes and data for a course in using the sequence assembly tools. These may be found in the 'course' subdirectory.

Note that only the "modern" programs have been ported to Windows (i.e. pregap4 and its ancilliary programs like vector_clip, screen_seq,..., trev, gap4, nip4 and sip4.) To complete the equivalence between the UNIX and Windows versions of the package we have removed all the "old" (mostly FORTRAN) programs from the UNIX release. These old programs (such as nip, sip,...) are now freely available to anyone as Digital UNIX, IRIX, Solaris and Linux binaries from our ftp site and will not be upgraded in the future. The Windows version will only be available through commercial distributors, but the UNIX versions will still be available directly from us at LMB.

A major change is the addition of a software licencing system. This means that the package can be made available to anybody in demonstration mode, and can be switched to full functionality with a key specific to that copy of the package on that machine. We can also provide temporary licence keys that will enable full functionality for a limited period. We plan for these temporary licences to be made available to applicants who simply fill in a web form.

To accompany the demo versions of the package we have included a set of data files. In demonstration mode, only these files can be loaded into the programs.

Program version numbers

Gap4 4.5

Nip4 1.2

Sip4 1.3

Pregap4 1.1

Trev 1.5

Operating systems

The binaries have been created in the following build environments. Typically newer environments for the same operating system should work fine, but not necessarily older systems. (For example, the binaries will not run under RedHat Linux 5.x)

Demo data sets

All pathnames listed below are relative to the installation root for the package.

Here is a list of sequences which may be loaded into Sip4.

For a good example of protein-protein similarity plots, try using mysa_drome.embl and mysa_human.embl.

For dna-protein plots, try using cemyo1.seq against mysa_caeel.seq.

To see how Sip4 handles large sequences try using ecoli.00003 and lambda.seq. This is a large comparison: 250Kb against 48.5Kb. Hence the slower searches, such as Find Similar Spans, will take a long time. We suggest searching with Find Matching Words using a word length of 12.

For Nip4, the following sequences are accepted.

Gap4 in demonstration mode only allows access to one data set at present. This has been base called with phred. The trace files may also be viewed in Trev.

This database is a section from a c.elegans cosmid, still in several contigs. You may try joining and editing contigs. The full functionality of Gap4 is available except for assembling or disassembling sequences.

For Pregap4 there is no demonstration mode. Pregap4 may be started and configured, but it will not process any data.

Sequence Library Access Using SRS

We have not upgraded our sequence library interface to SRS 6. and are aware of some problems in our use of SRS 5. We hope to include a Web based interface in a later release.

Linux, Gnome and Enlightenment

There is a known problem with the Gap4 contig editor when using Enlightenment as the window manager. This is the default for Gnome, but it is not known whether the problem arises when using Enlightenment in other environments. The symptom is that program will terminate instantly upon starting the contig editor with a complaint about X_ConfigureEvents.

The solution is to change window managers, which may be adjusted using the Gnome control panel.

Change log

Here is a list of changes since the 1999.0 (patched) release.



Bug fixes



Bug fixes



Bugs fixed






Bugs fixed



Bugs fixed

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