PPCMatrix, Oligo database, 4D Recording and Viewing software, Degoligo, LogoBar, VirtualWorm-Base


PPCMatrix is a versatile dotmatrix program for the Apple Macintosh, optimized for the PowerPC. It includes many additional features:

The special feature of the program is that it can read large (only limited by available memory) sequences, which can be translated in a special format, the 3-frame nested translation. The 3-frame nested translation can be compared against a protein sequence. Thus identifications of sequence similarities are possible even in case of frameshifts (due to sequence errors), or when exons are in different reading frames.

A description of this program has appeared in the journal Bioinformatics:
Thomas R. Bürglin (1998)
PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences.
Bioinformatics 14: 751-752.

The program is released on shareware basis. Current pricing is US$ 35 (checks, personal checks, or money orders drawn on US banks, or cash), 55 Swiss Francs (checks on Swiss banks in Swiss Francs) or 50 Swiss Francs (cash). Commercial companies please enquire.

Registered users will obtain a copy of the program that allows up to 600 sequences to be loaded (subject to available memory limitations). In addition, full documentation of all features is provided. Registered users will also receive bug fixes automatically by email as attachments.

This download version is fully functional, but limited to 5 sequences resident in memory. The archives are self-extracting. In addition to the program application, there are 2 files (xx.tables) which contain the translation tables and the matrixes and need to be in the same folder as the application. Furthermore, a README file is included. The program generates a Preferences file (PPCMatrix Prefs) in the same folder, if none is present.

The current version (June 2003) is PPCMatrixV1.25

Download PPCMatrix V1.25 for PowerPC

An old version for 68k machines can be downloaded here. It has not been updated since 1998.
Download PPCMatrix V1.01 for 68k machines.

To register please send an email to me. A full version of the software, as well as additional documentation will be provided by email.

Please report bugs and suggestions to Thomas R. Bürglin at:

Additional information for the program is provided here.

Oligo database

This is a Filemaker Pro database template to organize oligonucleotides. Many types of calculations are performed automatically.

It is available for free. Copyright Thomas R. Bürglin.

Download Oligo Database template

4D Recording and Viewing software

This software is for recording 4-dimensional image data from a microscope using the MacOS.

Ref.: Thomas R. Bürglin (2000) A 2-channel 4-dimensional image recording and viewing system with automatic drift correction. J. of Microscopy, 200, 75-78.

It is inspired, an partially compatible (the pics stack files) with the software from C. Thomas and J. White, see their Web site.

It offers two special features: recording in 2 channels (so fluorescence can be interspersed within DIC stacks),
and correction of microscope stage slippage with an software controlled drift correction.
The hardware setup consists of    a) any DIC & fluorscence microscope.
                                                     b) an ASI MFC-1 Z-axis drive and and an SC-2 dual shutter controller
                                                         attached to the microscope.
                                                     c) a Sony DXC-950 camera.
                                                     d) a Macintosh PowerPC with serial port to control the camera and the ASI devices.
                                                     e) a Scion CG-7 PCI framegrabber.

The software that controls this setup consists of 2 components:

a) Simple4DRecord macros, a set of macros for the Scion Image application that comes with the framegrabber.
    With this you record stacks, and 4D series.

b) Simple4DViewer, an application to view and annotate 4D series.

Instructions for operation are found in this MSWord file.


Degoligo is a small C program that runs in the terminal window of Mac Os X  (tested under 10.3).
The purpose of the program is to determine the probability of a degenerate oligonucleotide sequence under conditions of 0, 1, 2, 3, 4, or 5 mismatches.
For example, a degenerate oligonucleotide sequence is AARTCGYRG.
This sequence is 9 nucleotides long, and 8 fold degenerate.
The probability of this sequence is  3.05176e-05, which is 1 :  32768.
Thus, every 32768 nucleotides in average, you will find a match of this sequence in a genome (A,C,T,G are assumed to be equally represented with 25% each). So, in C. elegans (100 Million bases) you will find about 3051 matches to this degenerate oligo with 0 mismatches.
If mismatches are allowed (as can happen during hybridisation), then matches will occur of course more often. Hence the program also calculates the probabilities for up to 5 mismatches.

Download the program