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Version-2002.0 Release Notes

James Bonfield, Kathryn Beal, Yaping Cheng, Mark Jordan and Rodger Staden

The most visible additions to this release are our improved methods for automatic mutation detection and for the visualisation and reporting of mutations within Gap4. For more information on this topic we have prepared a separate web page demonstrating the new mutation features. This effects both Gap4 and Pregap4. (Be sure to remove (or edit) any pregap4.config or config.pg4 files to see the new modules listed within Pregap4.)

Other key changes include (i) there was a reading length limit of 30,000 bases in gap4, this has been removed so that "readings" of any length can now be assembled (as before the length of a contig is effectively unlimited); (ii) the ability to assemble EMBL format sequence files and their feature tables into gap4 databases; (iii) new program copy_reads for copying useful finishing data from one gap4 database to another; (iv) new program polyA_clip for trimming polyA/T from readings. A more detailed list of the program changes made is given below.

This is also the first official release of the MacOSX version (10.2) of the package. Initially we created and made available an Aqua version, but we felt this was too buggy (although many users said that having the functionality of our package available on the Mac made the bugs seem insignificant), so this version requires X11. See the Apple XFree86 site to download X11. As far as we have checked, the MacOSX-X11 version appears to be as bug-free as the other versions of the package. Many of the bugs in the Aqua version were in the Tk libraries and it looked as though fixes would require greater knowledge of the Mac than we possess. We would be interested to receive comments about fixing these bugs and the need for an Aqua version. As the Mac version was built on 10.2 we are not sure if it will work correctly with 10.1.

Our experiment suggestion / finishing program, now named "prefinish", is being used to help complete around 500 clones per month at the Wellcome Trust Sanger Institute. The program is still under development, but is clearly very useful, and we welcome requests from others interested in trying it.

A large number of bugs have been fixed in this release (some are listed below), many with the help of purify and valgrind.

Program version numbers

Operating systems

The binaries for this beta release 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, but will run on RedHat Linux 7.x)

Demo data sets

The course (see course/*_docs/*.pdf) may be run when in demonstration mode (ie without needing a licence). Specifically all demonstration data files are considered as valid sequences and so are exempt from the licence restrictions. All pathnames listed below are relative to the installation root for the package.

Here is a list of sequences which may be loaded into spin:

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

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

To see how spin 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.

Gap4 in demonstration mode allows access to:

Pregap4 in demonstration mode allows access to the same files listed for Gap4.

Change log

Here is a list of changes since the 2001.0 release.



Bug fixes



Bug fixes



Bug fixes



Bug fixes



Bug fixes


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URL: http://www.mrc-lmb.cam.ac.uk/pubseq/2002.0.html