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The MPI Bioinformatics Toolkit for protein sequence analysis - PubMed

️Sun Jan 01 2006

The MPI Bioinformatics Toolkit for protein sequence analysis

Andreas Biegert et al. Nucleic Acids Res. 2006.

Abstract

The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de.

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Figures

**Figure 1**
Input and result pages of PSI-BLAST with overlaid windows for genome databases and Jalview alignment viewer (32).

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References

1. Rost B., Liu J. The PredictProtein server. Nucleic Acids Res. 2003;31:3300–3304. - PMC - PubMed
1. Gracy J., Chiche L. PAT: a protein analysis toolkit for integrated biocomputing on the web. Nucleic Acids Res. 2005;33(Suppl. 2):W65–W71. - PMC - PubMed
1. Subramaniam S. The biology workbench—a seamless database and analysis environment for the biologist. Proteins. 1998;32:1–2. - PubMed
1. Badidi E., De Sousa C., Lang B., Burger G. Anabench: a web/corba-based workbench for biomolecular sequence analysis. BMC Bioinformatics. 2003;4:63. - PMC - PubMed
1. Söding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33:W244–W248. - PMC - PubMed

The MPI Bioinformatics Toolkit for protein sequence analysis - PubMed