Double Digester

What it is: Double Digester (DD) is a program to help molecular biologists make restriction maps from gel data. You give it fragment sizes from two different single restriction digests together with the fragments from the double digest done with both enzymes. Data entry can be done with the mouse, the keyboard or from a file. Using the mouse allows you to work directly from a picture of your gel. DD works on a Macintosh, and also on Unix using the X Window System (X11). With a few small exceptions, DD behaves the same on both platforms.

Current status: No further development seems likely, and the available versions have often-fatal incompatibilities with newer machines and environments -- e.g. the PowerMacs and Sun Solaris 2.x. Funding for the project ended a few years ago, the author has moved to a new job at the National Library of Medicine, and two pre-school kids leave no "spare time" in which to pursue such an effort. Some improvements were made to the Mac version in late 1994 and early 1995, and I have left notes below on various other improvements it would be nice to make, but all work is on hold for the foreseeable future.

Currently available: These resources continue to be used and found useful by some researchers. Those needing platforms or features not supported by Double Digester may wish to consult the following article

James Inglehart & Peter C. Nelson "On the limitations of automated restriction mapping" CABIOS Vol.10 No.3, pp 249-261

in which a number of programs are reviewed.

Articles etc.

• Cabios Article (pre-publication text; see Vol.10 No.4, 1994, pp.443-450).
• ReadMe file from ftp directory.
• Warning for SunOS 4.1.3 and Solaris.

Manual

• Local HyperText Access.
• ASCII Text version.
• DVI version (requires external viewer).
• Postscript version (requires external viewer).

Program (for file transfer)

• Sun version (compressed executable file).
• Macintosh version (binhexed self-extracting archive).
• HP-UX 7.0 version (compressed executable file).

Data Files (for file transfer)

• Sun & HP data directory (tar file).
• Mac data folder (binhexed self-extracting archive).

Program Updates (1.1 beta 3, Macintosh version)

After a long hiatus, I finally got around to some bug fixes and enhancements. The driving consideration was to quickly make available features needed by local labs, and thorough testing has not yet been carried out.
Changes:

• Scrolling constraint window: if font adjustments can't fit them all in, up/down buttons appear.
• Progress reports: Each stage of map building reports on progress in the Help window.

Pending:

• Incompatibilities with new hardware/software: DD currently crashes on the PowerMacs and Solaris 2 platforms I have tested, but I haven't had time to identify and correct these problems.
• Extend constraints handling: adjacency, overlap between fragments in the single-enzyme lanes, end-labels, vector and partial-digest data are all being worked on.
• Multiple enzymes: Ways to integrate multiple related sets of double digest data, as well as triple digests, are being examined.
• Data entry: New forms of data entry, setting scaling and error levels, associating notes with on-screen data, ... are also under review.
• Maps: Current thoughts include attempts to further summarize/analyze alternative maps and simultaneous display of multiple maps.

Available Versions:

• Macintosh version (binhexed stuffit archive).
• Sun version (not currently available).
• HP-UX (no longer supported).

The current version is 1.1 beta 2, completed March 1993. DD was created by Larry Wright; the manual was written by John Reinitz.

Last modified: 15 July 1996
Questions or Comments: EMail: webmaster@ycmiadm.med.yale.edu