The MPI Bioinformatics Toolkit for protein sequence analysis
Johannes Söding and
Andrei N. Lupas
Department of protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
Nucleic Acids Research 2006 34(Web Server issue):W335-W339; doi:10.1093/nar/gkl217.
The MPI Bioinformatics Toolkit is an interactive web servicewhich offers access to a great variety of public and in-housebioinformatics tools. They are grouped into different sectionsthat support sequence searches, multiple alignment, secondaryand tertiary structure prediction and classification. Severalpublic tools are offered in customized versions that extendtheir functionality. For example, PSI-BLAST can be run againstregularly updated standard databases, customized user databasesor selectable sets of genomes. Another tool, Quick2D, integratesthe results of various secondary structure, transmembrane anddisorder prediction programs into one view. The Toolkit providesa friendly and intuitive user interface with an online helpfacility. As a key feature, various tools are interconnectedso that the results of one tool can be forwarded to other tools.One could run PSI-BLAST, parse out a multiple alignment of selectedhits and send the results to a cluster analysis tool. The Toolkitframework and the tools developed in-house will be packagedand freely available under the GNU Lesser General Public Licence(LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de.