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Version-1996.2 Release Notes

This release sees many bug fixes, but few truely new features. The most noticable gap4 changes are the considerable speed improvements to gap4 and two new assembly engines (forthcoming). In addition new features include a new text based contig selector to supplement the existing graphical display, an improved check assembly function and the removal of a few size limitations.

The new assembly engines are Xiaoqiu Huang's CAP2 and Gene Myer's FAKII programs. For both of these we have the written the first versions of the gap4 interface. However we are not distributing either the Cap2 or FakII binaries and hence the Gap4 options are currently "greyed out". Both assembly systems have been modified to support Experiment Files. We hope to make a cap2 binary available ourselves soon. The mechanism of obtaining FAKII will be to obtain it direct from the authors, however our modified version is not yet available. Announcements for both will appear on the bionet.software.staden newsgroup when we are ready.

The second new assembly engine is Gene Myer's FAKII program. Once again, the Gap4 section is complete (first draft). We have made changes to the FAKII source code to output Experiment File format. At some (unspecified) later date the modified FAKII program will be available direct from Gene Myers.

For sip4 the most notable improvements, bug fixes excluded, are the ability to display alignments in a graphical fashion, the ability to now use personal sequence files of any length and to search them as libraries (entryname only), and a new exact match search in the sequence browser.

The trial versions of the programs that examine traces to determine where to clip readings based on their quality (trace_clip and scale_trace_clip) have been substantially altered.

Finally, several new programs are available. These are:

copy_db Copies and garbage collects gap4 databases.
extract_seq Extracts the sequence component from trace files or experiment files.
getABIstring Displays arbitrary string fields from an ABI trace file.
getABIcomment Displays the comments from an ABI trace file. Equivalent to getABIstring CMNT.
getABIdate Displays the run date from an ABI trace file.
get_scf_field Extracts data from the SCF comment section.
scf_info Displays details stored in the header of an SCF file.
scf_dump Displays the entire SCF file contents in a human readable format.
scf_update Converts between SCF file versions (2 to 3 and vice versa).
toad Relabels lanes in SCF traces.

Several programs have been removed. These are: bap, cop, cop-bap, dap, sapf, sipl, splitp1, splitp2, xbap, xdap and xsap.

The lookup command has been renamed to pregap_lookup.

Here follows a detailed, but not entirely complete, list of changes. The more important ones are displayed in bold text.


Speed and memory improvements

Contig Editor







Version-1996.2.1 Update

This consists of a minor update to 1996.2 containing a few bug fixes:

  1. Shuffle pads had a memory overflow that could occasionally corrupt the data within the editor. This does not directly corrupt the database permanently, but will do so if the data in the editor is then saved.

  2. Tags added to experiments files prior to assembly could be placed in the wrong location (by a few bases, depending on the number of pads to the reading). This only affects the normal shotgun assembly mode.

  3. The default font for the tk dialogue boxes does not exist on Solaris systems without the optional SUNWxwoft package installed. Changing the font from -Adobe-Times-... to -*-Times-... has hopefully fixed the problem.

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