ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ

The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/

X-HUSAR, an X-based graphical interface for the analysis of genomic sequences

Management and analysis of nucleotide and protein sequence and structure data constitute a traditional area of bioinformatics. Since the analytical programs are frequently developed by researchers, rather than software engineers, they tend to suffer from idiosyncratic and non-ergonomic man-machine interfaces. We report on HUSAR, our 140+ collection of third-party, as well as in-house developed or adapted, sequence manipulation and analysis tools, well integrated into the UNIX operating system environment and accessible via consistent menu-aware interface. Most of the HUSAR programs can be completely specified by UNIX command-line options; they can thus be run in batches or combined into pipes. Adding such a program into the HUSAR environment is almost a 'plug-and-play' exercise. HUSAR has been recently complemented with a graphical client interface, X-HUSAR, to support users on UNIX platforms with X11 windowing systems. The whole X-HUSAR interface is based on a single generic program, COMLIGEN, and a number of specific configuration files. COMLIGEN interprets those files and renders appropriate windows, menus, and other interactive elements, which help the end user in selecting application programs and specifying their options. Efforts of extending both HUSAR and X-HUSAR are roughly linear to the size of the collection.

A fast method for arranging DNA sequence fragments

A method is described which allows efficient arrangement of DNA sequence fragments and, based on this arrangement, reconstruction of a complete DNA sequence. The concepts and algorithms used are based on the mathematical theory of graphs. The amount of human interaction required is considerably reduced compared to existing methods. An experiment with a set of 168 fragments yields a DNA sequence of about 5800 bases almost automatically.

Computer programs for the analysis and the management of DNA sequences

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.