Welcome to Thomas Siegmund's Homepage

While at the Institute of Biology, Genetics, at the Free University of Berlin in the group of Günter Korge I was working on peptidergic neurons which regulate the development of the fruit fly Drosophila melanogaster. (See my paper Innervation of the ring gland for details.)

A completely different topic is a small family of Drosophila transcription factors containing the "pipsqueak" DNA binding domain. On the description of this domain I worked together with Michael Lehmann as well as on a screen for similar factors.

My teaching included the course "Biology for students of medicine" and the seminar "Introduction to the analysis of DNA and protein sequence data" for students of biology and biochemistry.

Nowadays I work as a bioinformatics specialist at DeveloGen.

Sequence analysis on the Linux desktop

Older commercial sequence analysis packages on MacOS or other semi-professional operating systems reach their limits rather quickly in the age of genome projects. Fortunately, there is a free alternative: Linux today is not only a robust server operating system, it can also be used quite comfortably as a desktop system. And there is a lot of high quality sequence analysis software available for Linux. One of the most prominent packages is EMBOSS, a collection of high-quality free Open Source software for sequence analysis. There are more than 160 applications in EMBOSS which provide the functionality for almost any task in day-to-day sequence analysis. EMBOSS is well documented, actively maintained and installs and runs without problems on any recent Linux system. There is only one problem: EMBOSS lacks a graphical user interface which allows the occasional user to access its functionality in an easy way. Therefore, I have built a simple GUI around the EMBOSS applications.

My favorite desktop is KDE, a graphical environment which runs on almost any variety of Unix, of course also on Linux. I used Kaptain (by Terek Zsolt ) for building KDE GUIs for EMBOSS applications. Kaptain is a universal graphical front-end for command line applications. It is a KDE application, but you can run it also from Gnome if at least the Qt libraries are installed.

For the 160+ applications in EMBOSS 5.0.0 (and for the PHYLIP 3.6b phylogeny package integrated in EMBOSS) I have written such Kaptain files, which can be started directly from the KDE desktop or from a shell. The files are interpreted by Kaptain, which in turn presents a nice dialog box with all options and parameters for a specific EMBOSS application. The user makes all necessary adjustments via mouse and keyboard and then runs the EMBOSS application from the dialog. A preview button allows to play with the settings until the best combination is found (*). Files can be selected by drag & drop or with the standard KDE file select box. The large number of options in the more complex EMBOSS applications are presented in a structured way. Tooltips for many checkboxes and buttons provide additional information about the application (as much as I can tell from the EMBOSS documentation).

To give you a first impression of the GUIs, I put some screenshots on a separate page.

If you like to use the grammars, you can download them here. You get them for free, but without any warranty. Additionally you will need a working KDE environment (or at least QT) and Kaptain. Both are installed by default on many recent linux systems. After the download you have to uncompress and untar the archive (tar xzvf kaptains.tar.gz) and to run the install.sh shell script within. Finally you need of course a working EMBOSS installation ;-).

If you find the grammars useful, please let me know (siegmund ( a t ) develogen ( d o t ) com). Of course any additions, critics and help are welcome.

(*) For the preview of text and sequence data and for the display of error messages I use Nedit, a fast, powerful and lightweight GUI text editor. Nedit is open source and and is included in many Linux distributions. With my .nedit settings file Nedit shows some common sequence file formats with a beautiful syntax highlighting. Especially for protein sequence alignments it is very useful to see the sequence in full colour. If you want to try it, backup the .nedit file in your home directory, download my .nedit file and put it into your home directory. If you do not like Nedit, you can of course modify the grammars to start any other editor.