This project is supported by a grant from the "Deutsche Forschungsgemeinschaft". It is part of the special program on Computational Methods for the Analysis and Interpretation of large genomic data sets.
This project is a collaboration of the Institute for Biophysics at the University of Düsseldorf and the Technical Faculty at the University of Bielefeld.
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Dr. Gerhard Steger steger@biophys.uni-duesseldorf.de Phone: +49-211-81-14927 Fax: +49-211-81-15167 |
Thermodynamic Prediction of Conserved Secondary Structure in RNA Thermodynamic stability of single-stranded nucleic acids Kinetic/sequential folding of single-stranded nucleic acids Search for and description of hybrid patterns
Optical denaturation curves Hydrodynamics
Viral RNAs Ribozymes |
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Stefan Gräf graef@biophys.uni-duesseldorf.de Phone: +49-211-81-14927 Fax: +49-211-81-15167 |
Temperature Gradient Gel Electrophoresis (TGGE) Development of hybrid patterns Linux Systems Formation of metastable RNA-structures via sequential folding of viroid-transcripts |
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Dr. Stefan Kurtz kurtz@techfak.uni-bielefeld.de Phone: +49-521-106-2910 Fax: +49-521-106-6411 |
Approximate Patterns Index Structures for Sequences (e.g. Suffix trees) Structural Patterns (e.g. repeats and palindroms) Implementation of Programming Languages |
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Dirk Strothmann dirks@techfak.uni-bielefeld.de Phone: +49-521-106-2914 Fax: +49-521-106-6411 |
Information Theory Hybrid Patterns |
We are currently developing HyPa which is a system for searching hybrid
patterns in large genomic datasets.
Hybrid patterns combine sequence similarities, structural similarities and
other user defined properties like thermodynamic constraints.
An important part of HyPa is HyPaL, the pattern matching language to
describe the hybrid patterns.
The database, called HyPaLib (for
Hybrid Pattern Library),
contains annotated structural elements characteristic for certain classes of
structural and/or functional RNAs. These elements are described in the language HyPaL specifically designed for this purpose.
The language allows to conveniently specify
hybrid patterns. We are
developing software tools that allow a user to search sequence
databases for any pattern in HyPaLib, thus providing functionality which is similar
to PROSITE, but dedicated to the more complex
patterns in RNA sequences.
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Documentation of HyPaL |
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HyPaLib Documentation |
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HyPaLib (HTML) |
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HyPaLib (TXT) |
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